[Avida-cvs] [avida-svn] r414 - in development: Avida.xcodeproj source source/analyze source/classification source/cpu source/event source/main source/tools source/utils
brysonda@myxo.css.msu.edu
brysonda at myxo.css.msu.edu
Wed Dec 7 15:55:29 PST 2005
Author: brysonda
Date: 2005-12-07 18:44:39 -0500 (Wed, 07 Dec 2005)
New Revision: 414
Removed:
development/source/classification/cGenotype_TestData.cc
development/source/classification/cInjectGenotype_BirthData.cc
development/source/event/cEventListIterator.cc
development/source/main/cMutation.cc
development/source/main/cReactionProcess.cc
development/source/main/cReactionRequisite.cc
development/source/main/cTaskEntry.cc
development/source/tools/cDataEntry.cc
development/source/tools/cFixedBlock.cc
development/source/tools/cRefBlock.cc
development/source/tools/cScaledBlock.cc
development/source/utils/fixHeaders.py
Modified:
development/Avida.xcodeproj/project.pbxproj
development/source/analyze/cAnalyze.cc
development/source/analyze/cAnalyze.h
development/source/analyze/cAnalyzeCommand.h
development/source/analyze/cAnalyzeCommandDef.h
development/source/analyze/cAnalyzeCommandDefBase.h
development/source/analyze/cAnalyzeFlowCommand.h
development/source/analyze/cAnalyzeFlowCommandDef.h
development/source/analyze/cAnalyzeFunction.h
development/source/analyze/cAnalyzeGenotype.cc
development/source/analyze/cAnalyzeGenotype.h
development/source/analyze/cAnalyzeUtil.cc
development/source/analyze/cAnalyzeUtil.h
development/source/analyze/cGenotypeBatch.h
development/source/classification/CMakeLists.txt
development/source/classification/cGenotype.cc
development/source/classification/cGenotype.h
development/source/classification/cGenotypeControl.cc
development/source/classification/cGenotypeControl.h
development/source/classification/cGenotype_BirthData.cc
development/source/classification/cGenotype_BirthData.h
development/source/classification/cGenotype_TestData.h
development/source/classification/cInjectGenotype.cc
development/source/classification/cInjectGenotypeElement.h
development/source/classification/cInjectGenotypeQueue.cc
development/source/classification/cInjectGenotypeQueue.h
development/source/classification/cInjectGenotype_BirthData.h
development/source/classification/cLineage.cc
development/source/classification/cLineage.h
development/source/classification/cSpecies.cc
development/source/classification/cSpecies.h
development/source/classification/cSpeciesControl.cc
development/source/classification/cSpeciesControl.h
development/source/classification/cSpeciesQueue.cc
development/source/classification/cSpeciesQueue.h
development/source/classification/nSpecies.h
development/source/cpu/cCPUMemory.cc
development/source/cpu/cCPUMemory.h
development/source/cpu/cCPUTestInfo.cc
development/source/cpu/cCPUTestInfo.h
development/source/cpu/cCodeLabel.cc
development/source/cpu/cCodeLabel.h
development/source/cpu/cHardware4Stack.cc
development/source/cpu/cHardware4Stack_Thread.cc
development/source/cpu/cHardware4Stack_Thread.h
development/source/cpu/cHardwareBase.cc
development/source/cpu/cHardwareBase.h
development/source/cpu/cHardwareCPU.cc
development/source/cpu/cHardwareCPU_Thread.cc
development/source/cpu/cHardwareCPU_Thread.h
development/source/cpu/cHardwareSMT.cc
development/source/cpu/cHardwareSMT_Thread.cc
development/source/cpu/cHardwareSMT_Thread.h
development/source/cpu/cHardwareStatusPrinter.cc
development/source/cpu/cHardwareStatusPrinter.h
development/source/cpu/cHardwareTracer.h
development/source/cpu/cHardwareTracer_4Stack.h
development/source/cpu/cHardwareTracer_CPU.h
development/source/cpu/cHardwareTracer_SMT.h
development/source/cpu/cHardwareTracer_TestCPU.h
development/source/cpu/cHeadCPU.cc
development/source/cpu/cHeadCPU.h
development/source/cpu/cHeadMultiMem.cc
development/source/cpu/cHeadMultiMem.h
development/source/cpu/cInstLibCPU.h
development/source/cpu/cMemoryFlags.h
development/source/cpu/cTestCPU.cc
development/source/cpu/cTestCPU.h
development/source/cpu/cTestUtil.cc
development/source/cpu/cTestUtil.h
development/source/cpu/nHardware4Stack.h
development/source/cpu/nHardwareCPU.h
development/source/cpu/nHardwareSMT.h
development/source/cpu/sCPUStats.h
development/source/cpu/tInstLib.h
development/source/defs.h
development/source/event/CMakeLists.txt
development/source/event/cEvent.h
development/source/event/cEventList.cc
development/source/event/cEventList.h
development/source/event/cEventListEntry.h
development/source/event/cEventListIterator.h
development/source/event/cEventManager.cc
development/source/event/cEventManager.h
development/source/event/cEventTriggers.cc
development/source/event/cEventTriggers.h
development/source/main/CMakeLists.txt
development/source/main/MyCodeArrayLessThan.h
development/source/main/avida.cc
development/source/main/avida.h
development/source/main/cAvidaConfig.cc
development/source/main/cAvidaDriver_Analyze.cc
development/source/main/cAvidaDriver_Analyze.h
development/source/main/cAvidaDriver_Base.cc
development/source/main/cAvidaDriver_Base.h
development/source/main/cAvidaDriver_Population.cc
development/source/main/cAvidaDriver_Population.h
development/source/main/cAvidaTriggers.h
development/source/main/cBirthChamber.cc
development/source/main/cBirthChamber.h
development/source/main/cEnvironment.cc
development/source/main/cEnvironment.h
development/source/main/cFitnessMatrix.cc
development/source/main/cFitnessMatrix.h
development/source/main/cGenome.cc
development/source/main/cGenome.h
development/source/main/cGenomeUtil.cc
development/source/main/cGenomeUtil.h
development/source/main/cInstLibBase.h
development/source/main/cInstSet.cc
development/source/main/cInstSet.h
development/source/main/cInstUtil.cc
development/source/main/cInstUtil.h
development/source/main/cInstruction.cc
development/source/main/cInstruction.h
development/source/main/cLandscape.cc
development/source/main/cLandscape.h
development/source/main/cLocalMutations.cc
development/source/main/cLocalMutations.h
development/source/main/cMutation.h
development/source/main/cMutationLib.cc
development/source/main/cMutationLib.h
development/source/main/cMutationRates.cc
development/source/main/cMutationRates.h
development/source/main/cMxCodeArray.cc
development/source/main/cMxCodeArray.h
development/source/main/cOrgMessage.cc
development/source/main/cOrgMessage.h
development/source/main/cOrganism.cc
development/source/main/cOrganism.h
development/source/main/cPhenotype.cc
development/source/main/cPhenotype.h
development/source/main/cPopulation.cc
development/source/main/cPopulation.h
development/source/main/cPopulationCell.cc
development/source/main/cPopulationCell.h
development/source/main/cPopulationInterface.cc
development/source/main/cPopulationInterface.h
development/source/main/cReaction.cc
development/source/main/cReaction.h
development/source/main/cReactionLib.cc
development/source/main/cReactionLib.h
development/source/main/cReactionProcess.h
development/source/main/cReactionRequisite.h
development/source/main/cReactionResult.cc
development/source/main/cReactionResult.h
development/source/main/cResource.cc
development/source/main/cResource.h
development/source/main/cResourceCount.cc
development/source/main/cResourceCount.h
development/source/main/cResourceLib.cc
development/source/main/cResourceLib.h
development/source/main/cSpatialCountElem.cc
development/source/main/cSpatialCountElem.h
development/source/main/cSpatialResCount.cc
development/source/main/cSpatialResCount.h
development/source/main/cStats.cc
development/source/main/cStats.h
development/source/main/cTaskEntry.h
development/source/main/cTaskLib.cc
development/source/main/cTaskLib.h
development/source/tools/CMakeLists.txt
development/source/tools/cBlockStruct.cc
development/source/tools/cBlockStruct.h
development/source/tools/cChangeList.cc
development/source/tools/cChangeList.h
development/source/tools/cConstSchedule.cc
development/source/tools/cConstSchedule.h
development/source/tools/cCountTracker.cc
development/source/tools/cCountTracker.h
development/source/tools/cCycleCheck.cc
development/source/tools/cCycleCheck.h
development/source/tools/cDataEntry.h
development/source/tools/cDataFile.cc
development/source/tools/cDataFile.h
development/source/tools/cDataFileManager.cc
development/source/tools/cDataManager_Base.cc
development/source/tools/cDataManager_Base.h
development/source/tools/cDefaultMessageDisplay.cc
development/source/tools/cDefaultMessageDisplay.h
development/source/tools/cDoubleSum.cc
development/source/tools/cDoubleSum.h
development/source/tools/cFile.cc
development/source/tools/cFile.h
development/source/tools/cFixedBlock.h
development/source/tools/cFixedCoords.h
development/source/tools/cGenesis.cc
development/source/tools/cGenesis.h
development/source/tools/cHelpAlias.cc
development/source/tools/cHelpAlias.h
development/source/tools/cHelpEntry.h
development/source/tools/cHelpFullEntry.h
development/source/tools/cHelpManager.cc
development/source/tools/cHelpManager.h
development/source/tools/cHelpType.cc
development/source/tools/cHelpType.h
development/source/tools/cHistogram.cc
development/source/tools/cHistogram.h
development/source/tools/cID.h
development/source/tools/cIndexedBlockStruct.cc
development/source/tools/cIndexedBlockStruct.h
development/source/tools/cInitFile.cc
development/source/tools/cInitFile.h
development/source/tools/cIntSum.cc
development/source/tools/cIntSum.h
development/source/tools/cIntegratedSchedule.cc
development/source/tools/cIntegratedSchedule.h
development/source/tools/cIntegratedScheduleNode.cc
development/source/tools/cIntegratedScheduleNode.h
development/source/tools/cMerit.cc
development/source/tools/cMerit.h
development/source/tools/cMessageClass.h
development/source/tools/cMessageClosure.h
development/source/tools/cMessageDisplay.cc
development/source/tools/cMessageDisplay.h
development/source/tools/cMessageDisplay_headers.h
development/source/tools/cMessageType.h
development/source/tools/cProbSchedule.cc
development/source/tools/cProbSchedule.h
development/source/tools/cRandom.cc
development/source/tools/cRandom.h
development/source/tools/cRefBlock.h
development/source/tools/cRunningAverage.cc
development/source/tools/cRunningAverage.h
development/source/tools/cScaledBlock.h
development/source/tools/cSchedule.cc
development/source/tools/cSchedule.h
development/source/tools/cString.cc
development/source/tools/cString.h
development/source/tools/cStringIterator.cc
development/source/tools/cStringIterator.h
development/source/tools/cStringList.cc
development/source/tools/cStringList.h
development/source/tools/cStringUtil.cc
development/source/tools/cStringUtil.h
development/source/tools/cTools.cc
development/source/tools/cTools.h
development/source/tools/cUInt.h
development/source/tools/cVerifierSuiteRecurser.h
development/source/tools/cWeightedIndex.cc
development/source/tools/cWeightedIndex.h
development/source/tools/functions.h
development/source/tools/tArgDataEntry.h
development/source/tools/tArray.h
development/source/tools/tBuffer.h
development/source/tools/tDataEntry.h
development/source/tools/tDataEntryBase.h
development/source/tools/tDataEntryCommand.h
development/source/tools/tDataManager.h
development/source/tools/tDictionary.h
development/source/tools/tHashTable.h
development/source/tools/tList.h
development/source/tools/tMatrix.h
development/source/tools/tMemTrack.h
development/source/tools/tObjectFactory.h
development/source/tools/tVector.h
development/source/tools/tVerifierSuite.hh
development/source/tools/win32_mkdir_hack.hh
Log:
Normalize copyright header comments and header include guards (most of them at least).
Modified: development/Avida.xcodeproj/project.pbxproj
===================================================================
--- development/Avida.xcodeproj/project.pbxproj 2005-12-07 21:01:20 UTC (rev 413)
+++ development/Avida.xcodeproj/project.pbxproj 2005-12-07 23:44:39 UTC (rev 414)
@@ -72,15 +72,12 @@
7053324C0929764C006BD186 /* cSpecies.cc in Sources */ = {isa = PBXBuildFile; fileRef = 705332480929764A006BD186 /* cSpecies.cc */; };
7053324D0929764E006BD186 /* cSpeciesQueue.cc in Sources */ = {isa = PBXBuildFile; fileRef = 7053324A0929764A006BD186 /* cSpeciesQueue.cc */; };
7053336D092A3DF9006BD186 /* cInjectGenotype.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70533364092A3DF4006BD186 /* cInjectGenotype.cc */; };
- 7053336E092A3DFB006BD186 /* cInjectGenotype_BirthData.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70533362092A3DF4006BD186 /* cInjectGenotype_BirthData.cc */; };
7053336F092A3DFC006BD186 /* cInjectGenotypeControl.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70533366092A3DF4006BD186 /* cInjectGenotypeControl.cc */; };
70533371092A3E00006BD186 /* cInjectGenotypeQueue.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70533369092A3DF4006BD186 /* cInjectGenotypeQueue.cc */; };
705333E7092A4B7F006BD186 /* cLineage.cc in Sources */ = {isa = PBXBuildFile; fileRef = 705333E5092A4B7C006BD186 /* cLineage.cc */; };
70533479092A4F4D006BD186 /* cGenotype_BirthData.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70F7DE700929678E009E311D /* cGenotype_BirthData.cc */; };
- 7053347A092A4F4F006BD186 /* cGenotype_TestData.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70F7DE720929678E009E311D /* cGenotype_TestData.cc */; };
7053347B092A4F50006BD186 /* cGenotypeControl.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70F7DE6809296613009E311D /* cGenotypeControl.cc */; };
7053347C092A4F52006BD186 /* cInjectGenotype.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70533364092A3DF4006BD186 /* cInjectGenotype.cc */; };
- 7053347D092A4F53006BD186 /* cInjectGenotype_BirthData.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70533362092A3DF4006BD186 /* cInjectGenotype_BirthData.cc */; };
7053347E092A4F55006BD186 /* cInjectGenotypeControl.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70533366092A3DF4006BD186 /* cInjectGenotypeControl.cc */; };
70533480092A4F59006BD186 /* cInjectGenotypeQueue.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70533369092A3DF4006BD186 /* cInjectGenotypeQueue.cc */; };
70533481092A4F5B006BD186 /* cLineage.cc in Sources */ = {isa = PBXBuildFile; fileRef = 705333E5092A4B7C006BD186 /* cLineage.cc */; };
@@ -96,12 +93,10 @@
706D33280854A90D00D7DC8F /* inst_set.smt in CopyFiles */ = {isa = PBXBuildFile; fileRef = 706D33270854A90D00D7DC8F /* inst_set.smt */; };
70B0865908F4974300FC65FE /* cLandscape.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0865108F4974300FC65FE /* cLandscape.cc */; };
70B0865C08F4974300FC65FE /* cLocalMutations.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0865408F4974300FC65FE /* cLocalMutations.cc */; };
- 70B0865D08F4974300FC65FE /* cMutation.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0865508F4974300FC65FE /* cMutation.cc */; };
70B0865E08F4974300FC65FE /* cMutationLib.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0865608F4974300FC65FE /* cMutationLib.cc */; };
70B0865F08F4974300FC65FE /* cMutationRates.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0865708F4974300FC65FE /* cMutationRates.cc */; };
70B0866108F4974300FC65FE /* cLandscape.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0865108F4974300FC65FE /* cLandscape.cc */; };
70B0866408F4974300FC65FE /* cLocalMutations.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0865408F4974300FC65FE /* cLocalMutations.cc */; };
- 70B0866508F4974300FC65FE /* cMutation.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0865508F4974300FC65FE /* cMutation.cc */; };
70B0866608F4974300FC65FE /* cMutationLib.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0865608F4974300FC65FE /* cMutationLib.cc */; };
70B0866708F4974300FC65FE /* cMutationRates.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0865708F4974300FC65FE /* cMutationRates.cc */; };
70B0866808F4974300FC65FE /* cMxCodeArray.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0865808F4974300FC65FE /* cMxCodeArray.cc */; };
@@ -117,8 +112,6 @@
70B0869E08F49F4800FC65FE /* cPhenotype.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0869C08F49F4800FC65FE /* cPhenotype.cc */; };
70B0872E08F5E82D00FC65FE /* cReaction.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0871E08F5E82D00FC65FE /* cReaction.cc */; };
70B0872F08F5E82D00FC65FE /* cReactionLib.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0871F08F5E82D00FC65FE /* cReactionLib.cc */; };
- 70B0873008F5E82D00FC65FE /* cReactionProcess.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0872008F5E82D00FC65FE /* cReactionProcess.cc */; };
- 70B0873108F5E82D00FC65FE /* cReactionRequisite.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0872108F5E82D00FC65FE /* cReactionRequisite.cc */; };
70B0873208F5E82D00FC65FE /* cReactionResult.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0872208F5E82D00FC65FE /* cReactionResult.cc */; };
70B0873308F5E82D00FC65FE /* cResource.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0872308F5E82D00FC65FE /* cResource.cc */; };
70B0873408F5E82D00FC65FE /* cResourceCount.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0872408F5E82D00FC65FE /* cResourceCount.cc */; };
@@ -126,12 +119,9 @@
70B0873608F5E82D00FC65FE /* cSpatialCountElem.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0872608F5E82D00FC65FE /* cSpatialCountElem.cc */; };
70B0873708F5E82D00FC65FE /* cSpatialResCount.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0872708F5E82D00FC65FE /* cSpatialResCount.cc */; };
70B0873B08F5E82D00FC65FE /* cStats.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0872B08F5E82D00FC65FE /* cStats.cc */; };
- 70B0873C08F5E82D00FC65FE /* cTaskEntry.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0872C08F5E82D00FC65FE /* cTaskEntry.cc */; };
70B0873D08F5E82D00FC65FE /* cTaskLib.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0872D08F5E82D00FC65FE /* cTaskLib.cc */; };
70B0873E08F5E82D00FC65FE /* cReaction.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0871E08F5E82D00FC65FE /* cReaction.cc */; };
70B0873F08F5E82D00FC65FE /* cReactionLib.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0871F08F5E82D00FC65FE /* cReactionLib.cc */; };
- 70B0874008F5E82D00FC65FE /* cReactionProcess.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0872008F5E82D00FC65FE /* cReactionProcess.cc */; };
- 70B0874108F5E82D00FC65FE /* cReactionRequisite.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0872108F5E82D00FC65FE /* cReactionRequisite.cc */; };
70B0874208F5E82D00FC65FE /* cReactionResult.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0872208F5E82D00FC65FE /* cReactionResult.cc */; };
70B0874308F5E82D00FC65FE /* cResource.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0872308F5E82D00FC65FE /* cResource.cc */; };
70B0874408F5E82D00FC65FE /* cResourceCount.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0872408F5E82D00FC65FE /* cResourceCount.cc */; };
@@ -139,7 +129,6 @@
70B0874608F5E82D00FC65FE /* cSpatialCountElem.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0872608F5E82D00FC65FE /* cSpatialCountElem.cc */; };
70B0874708F5E82D00FC65FE /* cSpatialResCount.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0872708F5E82D00FC65FE /* cSpatialResCount.cc */; };
70B0874B08F5E82D00FC65FE /* cStats.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0872B08F5E82D00FC65FE /* cStats.cc */; };
- 70B0874C08F5E82D00FC65FE /* cTaskEntry.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0872C08F5E82D00FC65FE /* cTaskEntry.cc */; };
70B0874D08F5E82D00FC65FE /* cTaskLib.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0872D08F5E82D00FC65FE /* cTaskLib.cc */; };
70B087E208F5F4BA00FC65FE /* cChangeList.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B087DF08F5F4BA00FC65FE /* cChangeList.cc */; };
70B087E308F5F4BA00FC65FE /* cConstSchedule.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B087E008F5F4BA00FC65FE /* cConstSchedule.cc */; };
@@ -147,13 +136,11 @@
70B087E508F5F4BA00FC65FE /* cChangeList.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B087DF08F5F4BA00FC65FE /* cChangeList.cc */; };
70B087E608F5F4BA00FC65FE /* cConstSchedule.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B087E008F5F4BA00FC65FE /* cConstSchedule.cc */; };
70B087E708F5F4BA00FC65FE /* cCountTracker.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B087E108F5F4BA00FC65FE /* cCountTracker.cc */; };
- 70B0885408F5FE5800FC65FE /* cDataEntry.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0884E08F5FE5800FC65FE /* cDataEntry.cc */; };
70B0885508F5FE5800FC65FE /* cDataFile.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0884F08F5FE5800FC65FE /* cDataFile.cc */; };
70B0885608F5FE5800FC65FE /* cDataFileManager.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0885008F5FE5800FC65FE /* cDataFileManager.cc */; };
70B0885708F5FE5800FC65FE /* cDataManager_Base.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0885108F5FE5800FC65FE /* cDataManager_Base.cc */; };
70B0885808F5FE5800FC65FE /* cDefaultMessageDisplay.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0885208F5FE5800FC65FE /* cDefaultMessageDisplay.cc */; };
70B0885908F5FE5800FC65FE /* cDoubleSum.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0885308F5FE5800FC65FE /* cDoubleSum.cc */; };
- 70B0885A08F5FE5800FC65FE /* cDataEntry.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0884E08F5FE5800FC65FE /* cDataEntry.cc */; };
70B0885B08F5FE5800FC65FE /* cDataFile.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0884F08F5FE5800FC65FE /* cDataFile.cc */; };
70B0885C08F5FE5800FC65FE /* cDataFileManager.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0885008F5FE5800FC65FE /* cDataFileManager.cc */; };
70B0885D08F5FE5800FC65FE /* cDataManager_Base.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0885108F5FE5800FC65FE /* cDataManager_Base.cc */; };
@@ -234,10 +221,8 @@
70C1F03808C3C71300F50912 /* cTestCPU.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70C1F02808C3C71300F50912 /* cTestCPU.cc */; };
70C1F03908C3C71300F50912 /* cTestUtil.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70C1F02908C3C71300F50912 /* cTestUtil.cc */; };
70C1F19408C6A11100F50912 /* cEventList.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70C1F18F08C6A11100F50912 /* cEventList.cc */; };
- 70C1F19508C6A11100F50912 /* cEventListIterator.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70C1F19008C6A11100F50912 /* cEventListIterator.cc */; };
70C1F19608C6A11100F50912 /* cEventTriggers.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70C1F19108C6A11100F50912 /* cEventTriggers.cc */; };
70C1F19908C6A11100F50912 /* cEventList.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70C1F18F08C6A11100F50912 /* cEventList.cc */; };
- 70C1F19A08C6A11100F50912 /* cEventListIterator.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70C1F19008C6A11100F50912 /* cEventListIterator.cc */; };
70C1F19B08C6A11100F50912 /* cEventTriggers.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70C1F19108C6A11100F50912 /* cEventTriggers.cc */; };
70C5BC6509059A970028A785 /* cWorld.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70C5BC6309059A970028A785 /* cWorld.cc */; };
70C5BC6709059A970028A785 /* cWorld.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70C5BC6309059A970028A785 /* cWorld.cc */; };
@@ -265,7 +250,6 @@
70F7DE6C09296615009E311D /* cGenotypeControl.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70F7DE6809296613009E311D /* cGenotypeControl.cc */; };
70F7DE6D09296616009E311D /* cSpeciesControl.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70F7DE6A09296613009E311D /* cSpeciesControl.cc */; };
70F7DE7409296794009E311D /* cGenotype_BirthData.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70F7DE700929678E009E311D /* cGenotype_BirthData.cc */; };
- 70F7DE7509296795009E311D /* cGenotype_TestData.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70F7DE720929678E009E311D /* cGenotype_TestData.cc */; };
DCC3166107628531008F7A48 /* avida.cc in Sources */ = {isa = PBXBuildFile; fileRef = DCC3109C0762539E008F7A48 /* avida.cc */; };
/* End PBXBuildFile section */
@@ -419,7 +403,6 @@
7053324A0929764A006BD186 /* cSpeciesQueue.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cSpeciesQueue.cc; sourceTree = "<group>"; };
7053324B0929764A006BD186 /* cSpeciesQueue.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cSpeciesQueue.h; sourceTree = "<group>"; };
7053325609297702006BD186 /* nSpecies.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = nSpecies.h; sourceTree = "<group>"; };
- 70533362092A3DF4006BD186 /* cInjectGenotype_BirthData.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cInjectGenotype_BirthData.cc; sourceTree = "<group>"; };
70533363092A3DF4006BD186 /* cInjectGenotype_BirthData.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cInjectGenotype_BirthData.h; sourceTree = "<group>"; };
70533364092A3DF4006BD186 /* cInjectGenotype.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cInjectGenotype.cc; sourceTree = "<group>"; };
70533365092A3DF4006BD186 /* cInjectGenotype.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cInjectGenotype.h; sourceTree = "<group>"; };
@@ -447,7 +430,6 @@
70B0865008F4972600FC65FE /* MyCodeArrayLessThan.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = MyCodeArrayLessThan.h; sourceTree = "<group>"; };
70B0865108F4974300FC65FE /* cLandscape.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cLandscape.cc; sourceTree = "<group>"; };
70B0865408F4974300FC65FE /* cLocalMutations.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cLocalMutations.cc; sourceTree = "<group>"; };
- 70B0865508F4974300FC65FE /* cMutation.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cMutation.cc; sourceTree = "<group>"; };
70B0865608F4974300FC65FE /* cMutationLib.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cMutationLib.cc; sourceTree = "<group>"; };
70B0865708F4974300FC65FE /* cMutationRates.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cMutationRates.cc; sourceTree = "<group>"; };
70B0865808F4974300FC65FE /* cMxCodeArray.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cMxCodeArray.cc; sourceTree = "<group>"; };
@@ -478,8 +460,6 @@
70B0871D08F5E81000FC65FE /* cTaskLib.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cTaskLib.h; sourceTree = "<group>"; };
70B0871E08F5E82D00FC65FE /* cReaction.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cReaction.cc; sourceTree = "<group>"; };
70B0871F08F5E82D00FC65FE /* cReactionLib.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cReactionLib.cc; sourceTree = "<group>"; };
- 70B0872008F5E82D00FC65FE /* cReactionProcess.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cReactionProcess.cc; sourceTree = "<group>"; };
- 70B0872108F5E82D00FC65FE /* cReactionRequisite.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cReactionRequisite.cc; sourceTree = "<group>"; };
70B0872208F5E82D00FC65FE /* cReactionResult.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cReactionResult.cc; sourceTree = "<group>"; };
70B0872308F5E82D00FC65FE /* cResource.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cResource.cc; sourceTree = "<group>"; };
70B0872408F5E82D00FC65FE /* cResourceCount.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cResourceCount.cc; sourceTree = "<group>"; };
@@ -487,7 +467,6 @@
70B0872608F5E82D00FC65FE /* cSpatialCountElem.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cSpatialCountElem.cc; sourceTree = "<group>"; };
70B0872708F5E82D00FC65FE /* cSpatialResCount.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cSpatialResCount.cc; sourceTree = "<group>"; };
70B0872B08F5E82D00FC65FE /* cStats.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cStats.cc; sourceTree = "<group>"; };
- 70B0872C08F5E82D00FC65FE /* cTaskEntry.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cTaskEntry.cc; sourceTree = "<group>"; };
70B0872D08F5E82D00FC65FE /* cTaskLib.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cTaskLib.cc; sourceTree = "<group>"; };
70B0875A08F5EC8900FC65FE /* nGeometry.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = nGeometry.h; sourceTree = "<group>"; };
70B0875C08F5ECBC00FC65FE /* nReaction.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = nReaction.h; sourceTree = "<group>"; };
@@ -508,14 +487,12 @@
70B0884B08F5FE4500FC65FE /* cDataManager_Base.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cDataManager_Base.h; sourceTree = "<group>"; };
70B0884C08F5FE4500FC65FE /* cDefaultMessageDisplay.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cDefaultMessageDisplay.h; sourceTree = "<group>"; };
70B0884D08F5FE4500FC65FE /* cDoubleSum.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cDoubleSum.h; sourceTree = "<group>"; };
- 70B0884E08F5FE5800FC65FE /* cDataEntry.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cDataEntry.cc; sourceTree = "<group>"; };
70B0884F08F5FE5800FC65FE /* cDataFile.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cDataFile.cc; sourceTree = "<group>"; };
70B0885008F5FE5800FC65FE /* cDataFileManager.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cDataFileManager.cc; sourceTree = "<group>"; };
70B0885108F5FE5800FC65FE /* cDataManager_Base.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cDataManager_Base.cc; sourceTree = "<group>"; };
70B0885208F5FE5800FC65FE /* cDefaultMessageDisplay.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cDefaultMessageDisplay.cc; sourceTree = "<group>"; };
70B0885308F5FE5800FC65FE /* cDoubleSum.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cDoubleSum.cc; sourceTree = "<group>"; };
70B0887D08F603C600FC65FE /* cFile.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cFile.h; sourceTree = "<group>"; };
- 70B0887E08F603C600FC65FE /* cFixedBlock.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cFixedBlock.cc; sourceTree = "<group>"; };
70B0887F08F603C600FC65FE /* cFixedBlock.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cFixedBlock.h; sourceTree = "<group>"; };
70B0888008F603C600FC65FE /* cFixedCoords.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cFixedCoords.h; sourceTree = "<group>"; };
70B0888108F603C600FC65FE /* cGenesis.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cGenesis.h; sourceTree = "<group>"; };
@@ -543,10 +520,8 @@
70B0890908F762EA00FC65FE /* cMessageType.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cMessageType.h; sourceTree = "<group>"; };
70B0890A08F762EA00FC65FE /* cProbSchedule.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cProbSchedule.h; sourceTree = "<group>"; };
70B0890B08F762EA00FC65FE /* cRandom.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cRandom.h; sourceTree = "<group>"; };
- 70B0890C08F762EA00FC65FE /* cRefBlock.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cRefBlock.cc; sourceTree = "<group>"; };
70B0890D08F762EA00FC65FE /* cRefBlock.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cRefBlock.h; sourceTree = "<group>"; };
70B0890E08F762EA00FC65FE /* cRunningAverage.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cRunningAverage.h; sourceTree = "<group>"; };
- 70B0890F08F762EA00FC65FE /* cScaledBlock.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cScaledBlock.cc; sourceTree = "<group>"; };
70B0891008F762EA00FC65FE /* cScaledBlock.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cScaledBlock.h; sourceTree = "<group>"; };
70B0891108F762EA00FC65FE /* cSchedule.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cSchedule.h; sourceTree = "<group>"; };
70B0891208F762EA00FC65FE /* cString.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cString.h; sourceTree = "<group>"; };
@@ -637,7 +612,6 @@
70C1F18A08C6A0FA00F50912 /* cEventListIterator.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cEventListIterator.h; sourceTree = "<group>"; };
70C1F18B08C6A0FA00F50912 /* cEventTriggers.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cEventTriggers.h; sourceTree = "<group>"; };
70C1F18F08C6A11100F50912 /* cEventList.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cEventList.cc; sourceTree = "<group>"; };
- 70C1F19008C6A11100F50912 /* cEventListIterator.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cEventListIterator.cc; sourceTree = "<group>"; };
70C1F19108C6A11100F50912 /* cEventTriggers.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cEventTriggers.cc; sourceTree = "<group>"; };
70C5BC6209059A970028A785 /* cWorld.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cWorld.h; sourceTree = "<group>"; };
70C5BC6309059A970028A785 /* cWorld.cc */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = cWorld.cc; sourceTree = "<group>"; };
@@ -666,7 +640,6 @@
70F7DE6B09296613009E311D /* cSpeciesControl.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cSpeciesControl.h; sourceTree = "<group>"; };
70F7DE700929678E009E311D /* cGenotype_BirthData.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cGenotype_BirthData.cc; sourceTree = "<group>"; };
70F7DE710929678E009E311D /* cGenotype_BirthData.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cGenotype_BirthData.h; sourceTree = "<group>"; };
- 70F7DE720929678E009E311D /* cGenotype_TestData.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cGenotype_TestData.cc; sourceTree = "<group>"; };
70F7DE730929678E009E311D /* cGenotype_TestData.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cGenotype_TestData.h; sourceTree = "<group>"; };
70F7DE76092967A8009E311D /* cGenotypeBatch.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cGenotypeBatch.h; sourceTree = "<group>"; };
70FB86A908BFAFEC00BDF589 /* CMakeLists.txt */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = CMakeLists.txt; sourceTree = "<group>"; };
@@ -762,7 +735,6 @@
DCC315B0076253A5008F7A48 /* tVerifierSuite.hh */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.h; path = tVerifierSuite.hh; sourceTree = "<group>"; };
DCC315B1076253A5008F7A48 /* tVerifierSuiteRecurser.hh */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.h; path = tVerifierSuiteRecurser.hh; sourceTree = "<group>"; };
DCC315B5076253A5008F7A48 /* win32_mkdir_hack.hh */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.h; path = win32_mkdir_hack.hh; sourceTree = "<group>"; };
- DCC315BB076253A5008F7A48 /* fixHeaders.py */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text.script.python; path = fixHeaders.py; sourceTree = "<group>"; };
DCC315C1076253A5008F7A48 /* hist_map.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = hist_map.cc; sourceTree = "<group>"; };
DCC315C2076253A5008F7A48 /* hist_map2.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = hist_map2.cc; sourceTree = "<group>"; };
DCC315C3076253A5008F7A48 /* Makefile */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.make; path = Makefile; sourceTree = "<group>"; };
@@ -859,7 +831,6 @@
children = (
705333E5092A4B7C006BD186 /* cLineage.cc */,
705333E6092A4B7C006BD186 /* cLineage.h */,
- 70533362092A3DF4006BD186 /* cInjectGenotype_BirthData.cc */,
70533363092A3DF4006BD186 /* cInjectGenotype_BirthData.h */,
70533364092A3DF4006BD186 /* cInjectGenotype.cc */,
70533365092A3DF4006BD186 /* cInjectGenotype.h */,
@@ -877,7 +848,6 @@
7053324B0929764A006BD186 /* cSpeciesQueue.h */,
70F7DE700929678E009E311D /* cGenotype_BirthData.cc */,
70F7DE710929678E009E311D /* cGenotype_BirthData.h */,
- 70F7DE720929678E009E311D /* cGenotype_TestData.cc */,
70F7DE730929678E009E311D /* cGenotype_TestData.h */,
70F7DE6809296613009E311D /* cGenotypeControl.cc */,
70F7DE6909296613009E311D /* cGenotypeControl.h */,
@@ -895,15 +865,17 @@
DCC30C490762532C008F7A48 = {
isa = PBXGroup;
children = (
- DCC30C670762539A008F7A48 /* Source */,
- 70FB86A908BFAFEC00BDF589 /* CMakeLists.txt */,
+ DCC30C670762539A008F7A48 /* Main Source */,
+ DCC3113A0762539E008F7A48 /* Support */,
+ DCC315B6076253A5008F7A48 /* Utilities */,
DCC3164E07626CF3008F7A48 /* Products */,
+ 70FB86A908BFAFEC00BDF589 /* CMakeLists.txt */,
70658C59085DF67D00486BED /* libncurses.5.4.dylib */,
703F684207B437B800C1CA76 /* status.xml */,
);
sourceTree = "<group>";
};
- DCC30C670762539A008F7A48 /* Source */ = {
+ DCC30C670762539A008F7A48 /* Main Source */ = {
isa = PBXGroup;
children = (
70422A1B091B141000A5E67F /* analyze */,
@@ -911,16 +883,14 @@
DCC30F7C0762539D008F7A48 /* cpu */,
DCC30FD00762539D008F7A48 /* event */,
DCC310040762539D008F7A48 /* main */,
- DCC3113A0762539E008F7A48 /* support */,
DCC31340076253A0008F7A48 /* third-party */,
DCC314D8076253A2008F7A48 /* tools */,
- DCC315B6076253A5008F7A48 /* utils */,
704866B2090B51310048600A /* viewer */,
DCC30F7B0762539D008F7A48 /* CMakeLists.txt */,
701384A10902A16F0087ED2E /* defs.h */,
DCC30FCF0762539D008F7A48 /* Doxyfile */,
);
- name = Source;
+ name = "Main Source";
path = source;
sourceTree = "<group>";
};
@@ -986,7 +956,6 @@
70C1F18F08C6A11100F50912 /* cEventList.cc */,
70C1F18808C6A0FA00F50912 /* cEventList.h */,
70C1F18908C6A0FA00F50912 /* cEventListEntry.h */,
- 70C1F19008C6A11100F50912 /* cEventListIterator.cc */,
70C1F18A08C6A0FA00F50912 /* cEventListIterator.h */,
7040CF1A0906A52E00AA820F /* cEventManager.cc */,
7040CF1B0906A52E00AA820F /* cEventManager.h */,
@@ -1032,7 +1001,6 @@
70B0864808F4972600FC65FE /* cLandscape.h */,
70B0865408F4974300FC65FE /* cLocalMutations.cc */,
70B0864B08F4972600FC65FE /* cLocalMutations.h */,
- 70B0865508F4974300FC65FE /* cMutation.cc */,
70B0864C08F4972600FC65FE /* cMutation.h */,
70B0865608F4974300FC65FE /* cMutationLib.cc */,
70B0864D08F4972600FC65FE /* cMutationLib.h */,
@@ -1056,9 +1024,7 @@
70B0870E08F5E81000FC65FE /* cReaction.h */,
70B0871F08F5E82D00FC65FE /* cReactionLib.cc */,
70B0870F08F5E81000FC65FE /* cReactionLib.h */,
- 70B0872008F5E82D00FC65FE /* cReactionProcess.cc */,
70B0871008F5E81000FC65FE /* cReactionProcess.h */,
- 70B0872108F5E82D00FC65FE /* cReactionRequisite.cc */,
70B0871108F5E81000FC65FE /* cReactionRequisite.h */,
70B0872208F5E82D00FC65FE /* cReactionResult.cc */,
70B0871208F5E81000FC65FE /* cReactionResult.h */,
@@ -1074,7 +1040,6 @@
70B0871708F5E81000FC65FE /* cSpatialResCount.h */,
70B0872B08F5E82D00FC65FE /* cStats.cc */,
70B0871B08F5E81000FC65FE /* cStats.h */,
- 70B0872C08F5E82D00FC65FE /* cTaskEntry.cc */,
70B0871C08F5E81000FC65FE /* cTaskEntry.h */,
70B0872D08F5E82D00FC65FE /* cTaskLib.cc */,
70B0871D08F5E81000FC65FE /* cTaskLib.h */,
@@ -1090,7 +1055,7 @@
path = main;
sourceTree = "<group>";
};
- DCC3113A0762539E008F7A48 /* support */ = {
+ DCC3113A0762539E008F7A48 /* Support */ = {
isa = PBXGroup;
children = (
701384330900A45B0087ED2E /* organism.smtx */,
@@ -1111,7 +1076,8 @@
DCC3118C0762539F008F7A48 /* preset_organisms */,
7013852C0902E36B0087ED2E /* avida.cfg */,
);
- path = support;
+ name = Support;
+ path = source/support;
sourceTree = "<group>";
};
DCC3114D0762539E008F7A48 /* config */ = {
@@ -1280,10 +1246,8 @@
70B0890908F762EA00FC65FE /* cMessageType.h */,
70B0890A08F762EA00FC65FE /* cProbSchedule.h */,
70B0890B08F762EA00FC65FE /* cRandom.h */,
- 70B0890C08F762EA00FC65FE /* cRefBlock.cc */,
70B0890D08F762EA00FC65FE /* cRefBlock.h */,
70B0890E08F762EA00FC65FE /* cRunningAverage.h */,
- 70B0890F08F762EA00FC65FE /* cScaledBlock.cc */,
70B0891008F762EA00FC65FE /* cScaledBlock.h */,
70B0891108F762EA00FC65FE /* cSchedule.h */,
70B0891208F762EA00FC65FE /* cString.h */,
@@ -1293,12 +1257,10 @@
70B0888308F603D400FC65FE /* cFile.cc */,
70B0888408F603D400FC65FE /* cGenesis.cc */,
70B0887D08F603C600FC65FE /* cFile.h */,
- 70B0887E08F603C600FC65FE /* cFixedBlock.cc */,
70B0887F08F603C600FC65FE /* cFixedBlock.h */,
70B0888008F603C600FC65FE /* cFixedCoords.h */,
70B0888108F603C600FC65FE /* cGenesis.h */,
70B0888208F603C600FC65FE /* functions.h */,
- 70B0884E08F5FE5800FC65FE /* cDataEntry.cc */,
70B0884F08F5FE5800FC65FE /* cDataFile.cc */,
70B0885008F5FE5800FC65FE /* cDataFileManager.cc */,
70B0885108F5FE5800FC65FE /* cDataManager_Base.cc */,
@@ -1346,15 +1308,15 @@
path = tests;
sourceTree = "<group>";
};
- DCC315B6076253A5008F7A48 /* utils */ = {
+ DCC315B6076253A5008F7A48 /* Utilities */ = {
isa = PBXGroup;
children = (
- DCC315BB076253A5008F7A48 /* fixHeaders.py */,
DCC315BC076253A5008F7A48 /* hist_map */,
DCC315C4076253A5008F7A48 /* matlabify.cc */,
DCC315C5076253A5008F7A48 /* task_events */,
);
- path = utils;
+ name = Utilities;
+ path = source/utils;
sourceTree = "<group>";
};
DCC315BC076253A5008F7A48 /* hist_map */ = {
@@ -1545,7 +1507,6 @@
70C1F03808C3C71300F50912 /* cTestCPU.cc in Sources */,
70C1F03908C3C71300F50912 /* cTestUtil.cc in Sources */,
70C1F19908C6A11100F50912 /* cEventList.cc in Sources */,
- 70C1F19A08C6A11100F50912 /* cEventListIterator.cc in Sources */,
70C1F19B08C6A11100F50912 /* cEventTriggers.cc in Sources */,
702D4F0308DA5341007BA469 /* cAvidaDriver_Analyze.cc in Sources */,
702D4F0408DA5341007BA469 /* cAvidaDriver_Base.cc in Sources */,
@@ -1561,7 +1522,6 @@
70CA6EE108DB7F8200068AC2 /* cInstUtil.cc in Sources */,
70B0866108F4974300FC65FE /* cLandscape.cc in Sources */,
70B0866408F4974300FC65FE /* cLocalMutations.cc in Sources */,
- 70B0866508F4974300FC65FE /* cMutation.cc in Sources */,
70B0866608F4974300FC65FE /* cMutationLib.cc in Sources */,
70B0866708F4974300FC65FE /* cMutationRates.cc in Sources */,
70B0866808F4974300FC65FE /* cMxCodeArray.cc in Sources */,
@@ -1572,8 +1532,6 @@
70B0869E08F49F4800FC65FE /* cPhenotype.cc in Sources */,
70B0873E08F5E82D00FC65FE /* cReaction.cc in Sources */,
70B0873F08F5E82D00FC65FE /* cReactionLib.cc in Sources */,
- 70B0874008F5E82D00FC65FE /* cReactionProcess.cc in Sources */,
- 70B0874108F5E82D00FC65FE /* cReactionRequisite.cc in Sources */,
70B0874208F5E82D00FC65FE /* cReactionResult.cc in Sources */,
70B0874308F5E82D00FC65FE /* cResource.cc in Sources */,
70B0874408F5E82D00FC65FE /* cResourceCount.cc in Sources */,
@@ -1581,12 +1539,10 @@
70B0874608F5E82D00FC65FE /* cSpatialCountElem.cc in Sources */,
70B0874708F5E82D00FC65FE /* cSpatialResCount.cc in Sources */,
70B0874B08F5E82D00FC65FE /* cStats.cc in Sources */,
- 70B0874C08F5E82D00FC65FE /* cTaskEntry.cc in Sources */,
70B0874D08F5E82D00FC65FE /* cTaskLib.cc in Sources */,
70B087E508F5F4BA00FC65FE /* cChangeList.cc in Sources */,
70B087E608F5F4BA00FC65FE /* cConstSchedule.cc in Sources */,
70B087E708F5F4BA00FC65FE /* cCountTracker.cc in Sources */,
- 70B0885A08F5FE5800FC65FE /* cDataEntry.cc in Sources */,
70B0885B08F5FE5800FC65FE /* cDataFile.cc in Sources */,
70B0885C08F5FE5800FC65FE /* cDataFileManager.cc in Sources */,
70B0885D08F5FE5800FC65FE /* cDataManager_Base.cc in Sources */,
@@ -1638,10 +1594,8 @@
70F7DCA009293E76009E311D /* cClassificationManager.cc in Sources */,
70F7DCA109293E77009E311D /* cGenotype.cc in Sources */,
70533479092A4F4D006BD186 /* cGenotype_BirthData.cc in Sources */,
- 7053347A092A4F4F006BD186 /* cGenotype_TestData.cc in Sources */,
7053347B092A4F50006BD186 /* cGenotypeControl.cc in Sources */,
7053347C092A4F52006BD186 /* cInjectGenotype.cc in Sources */,
- 7053347D092A4F53006BD186 /* cInjectGenotype_BirthData.cc in Sources */,
7053347E092A4F55006BD186 /* cInjectGenotypeControl.cc in Sources */,
70533480092A4F59006BD186 /* cInjectGenotypeQueue.cc in Sources */,
70533481092A4F5B006BD186 /* cLineage.cc in Sources */,
@@ -1677,7 +1631,6 @@
70C1F03008C3C71300F50912 /* cTestCPU.cc in Sources */,
70C1F03108C3C71300F50912 /* cTestUtil.cc in Sources */,
70C1F19408C6A11100F50912 /* cEventList.cc in Sources */,
- 70C1F19508C6A11100F50912 /* cEventListIterator.cc in Sources */,
70C1F19608C6A11100F50912 /* cEventTriggers.cc in Sources */,
702D4EFF08DA5341007BA469 /* cAvidaDriver_Base.cc in Sources */,
702D4F0008DA5341007BA469 /* cAvidaDriver_Population.cc in Sources */,
@@ -1691,7 +1644,6 @@
70CA6ED108DB7F8200068AC2 /* cInstUtil.cc in Sources */,
70B0865908F4974300FC65FE /* cLandscape.cc in Sources */,
70B0865C08F4974300FC65FE /* cLocalMutations.cc in Sources */,
- 70B0865D08F4974300FC65FE /* cMutation.cc in Sources */,
70B0865E08F4974300FC65FE /* cMutationLib.cc in Sources */,
70B0865F08F4974300FC65FE /* cMutationRates.cc in Sources */,
70B0868B08F49EA800FC65FE /* cOrganism.cc in Sources */,
@@ -1701,8 +1653,6 @@
70B0869D08F49F4800FC65FE /* cPhenotype.cc in Sources */,
70B0872E08F5E82D00FC65FE /* cReaction.cc in Sources */,
70B0872F08F5E82D00FC65FE /* cReactionLib.cc in Sources */,
- 70B0873008F5E82D00FC65FE /* cReactionProcess.cc in Sources */,
- 70B0873108F5E82D00FC65FE /* cReactionRequisite.cc in Sources */,
70B0873208F5E82D00FC65FE /* cReactionResult.cc in Sources */,
70B0873308F5E82D00FC65FE /* cResource.cc in Sources */,
70B0873408F5E82D00FC65FE /* cResourceCount.cc in Sources */,
@@ -1710,12 +1660,10 @@
70B0873608F5E82D00FC65FE /* cSpatialCountElem.cc in Sources */,
70B0873708F5E82D00FC65FE /* cSpatialResCount.cc in Sources */,
70B0873B08F5E82D00FC65FE /* cStats.cc in Sources */,
- 70B0873C08F5E82D00FC65FE /* cTaskEntry.cc in Sources */,
70B0873D08F5E82D00FC65FE /* cTaskLib.cc in Sources */,
70B087E208F5F4BA00FC65FE /* cChangeList.cc in Sources */,
70B087E308F5F4BA00FC65FE /* cConstSchedule.cc in Sources */,
70B087E408F5F4BA00FC65FE /* cCountTracker.cc in Sources */,
- 70B0885408F5FE5800FC65FE /* cDataEntry.cc in Sources */,
70B0885508F5FE5800FC65FE /* cDataFile.cc in Sources */,
70B0885608F5FE5800FC65FE /* cDataFileManager.cc in Sources */,
70B0885708F5FE5800FC65FE /* cDataManager_Base.cc in Sources */,
@@ -1757,11 +1705,9 @@
70F7DE6C09296615009E311D /* cGenotypeControl.cc in Sources */,
70F7DE6D09296616009E311D /* cSpeciesControl.cc in Sources */,
70F7DE7409296794009E311D /* cGenotype_BirthData.cc in Sources */,
- 70F7DE7509296795009E311D /* cGenotype_TestData.cc in Sources */,
7053324C0929764C006BD186 /* cSpecies.cc in Sources */,
7053324D0929764E006BD186 /* cSpeciesQueue.cc in Sources */,
7053336D092A3DF9006BD186 /* cInjectGenotype.cc in Sources */,
- 7053336E092A3DFB006BD186 /* cInjectGenotype_BirthData.cc in Sources */,
7053336F092A3DFC006BD186 /* cInjectGenotypeControl.cc in Sources */,
70533371092A3E00006BD186 /* cInjectGenotypeQueue.cc in Sources */,
705333E7092A4B7F006BD186 /* cLineage.cc in Sources */,
@@ -1800,7 +1746,7 @@
};
name = Development;
};
- 700E2B80085DE50C00CF158A /* Deployment */ = {
+ 700E2B80085DE50C00CF158A /* Deployment-G4 */ = {
isa = XCBuildConfiguration;
buildSettings = {
COPY_PHASE_STRIP = YES;
@@ -1827,25 +1773,40 @@
);
ZERO_LINK = NO;
};
- name = Deployment;
+ name = "Deployment-G4";
};
- 700E2B81085DE50C00CF158A /* Profile */ = {
+ 702442D30859E0B00059BD9B /* Development */ = {
isa = XCBuildConfiguration;
buildSettings = {
+ GCC_MODEL_CPU = G4;
+ PRODUCT_NAME = primitive;
+ };
+ name = Development;
+ };
+ 702442D40859E0B00059BD9B /* Deployment-G4 */ = {
+ isa = XCBuildConfiguration;
+ buildSettings = {
+ GCC_MODEL_CPU = G4;
+ PRODUCT_NAME = primitive;
+ };
+ name = "Deployment-G4";
+ };
+ 702442D80859E0B00059BD9B /* Development */ = {
+ isa = XCBuildConfiguration;
+ buildSettings = {
GCC_ALTIVEC_EXTENSIONS = YES;
GCC_AUTO_VECTORIZATION = YES;
GCC_DEBUGGING_SYMBOLS = full;
+ GCC_DYNAMIC_NO_PIC = YES;
GCC_ENABLE_FIX_AND_CONTINUE = YES;
GCC_FAST_MATH = YES;
- GCC_MODEL_CPU = G4;
- GCC_OPTIMIZATION_LEVEL = 3;
- GCC_PREPROCESSOR_DEFINITIONS = REVISION_SUPPORT;
+ GCC_OPTIMIZATION_LEVEL = 0;
+ GCC_PREPROCESSOR_DEFINITIONS = (
+ DEBUG,
+ REVISION_SUPPORT,
+ );
GCC_UNROLL_LOOPS = YES;
- HEADER_SEARCH_PATHS = source/event/;
- INSTALL_PATH = "$(BUILT_PRODUCTS_DIR)/work";
- LIBRARY_SEARCH_PATHS = "";
- PRODUCT_NAME = viewer;
- SKIP_INSTALL = YES;
+ GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
WARNING_CFLAGS = (
"-Wmost",
"-Wno-four-char-constants",
@@ -1853,39 +1814,49 @@
);
ZERO_LINK = YES;
};
- name = Profile;
+ name = Development;
};
- 702442D30859E0B00059BD9B /* Development */ = {
+ 702442D90859E0B00059BD9B /* Deployment-G4 */ = {
isa = XCBuildConfiguration;
buildSettings = {
+ DEPLOYMENT_POSTPROCESSING = YES;
GCC_ALTIVEC_EXTENSIONS = YES;
GCC_AUTO_VECTORIZATION = YES;
- GCC_DEBUGGING_SYMBOLS = full;
- GCC_ENABLE_FIX_AND_CONTINUE = YES;
+ GCC_DYNAMIC_NO_PIC = YES;
GCC_FAST_MATH = YES;
- GCC_MODEL_CPU = G4;
- GCC_OPTIMIZATION_LEVEL = 0;
+ GCC_OPTIMIZATION_LEVEL = 3;
GCC_PREPROCESSOR_DEFINITIONS = (
- DEBUG,
+ NDEBUG,
REVISION_SUPPORT,
);
GCC_UNROLL_LOOPS = YES;
- HEADER_SEARCH_PATHS = source/event/;
- INSTALL_PATH = "$(BUILT_PRODUCTS_DIR)/work";
- PRODUCT_NAME = primitive;
- SKIP_INSTALL = YES;
WARNING_CFLAGS = (
"-Wmost",
"-Wno-four-char-constants",
"-Wno-unknown-pragmas",
);
- ZERO_LINK = YES;
};
- name = Development;
+ name = "Deployment-G4";
};
- 702442D40859E0B00059BD9B /* Deployment */ = {
+ 70B393DC0944CA6F0018F09D /* Deployment-G5 */ = {
isa = XCBuildConfiguration;
buildSettings = {
+ GCC_MODEL_CPU = G4;
+ PRODUCT_NAME = primitive;
+ };
+ name = "Deployment-G5";
+ };
+ 70B393DD0944CA6F0018F09D /* Profile */ = {
+ isa = XCBuildConfiguration;
+ buildSettings = {
+ GCC_MODEL_CPU = G4;
+ PRODUCT_NAME = primitive;
+ };
+ name = Profile;
+ };
+ 70B393DE0944CA6F0018F09D /* Deployment-G5 */ = {
+ isa = XCBuildConfiguration;
+ buildSettings = {
COPY_PHASE_STRIP = YES;
DEAD_CODE_STRIPPING = YES;
GCC_ALTIVEC_EXTENSIONS = YES;
@@ -1896,14 +1867,12 @@
GCC_GENERATE_DEBUGGING_SYMBOLS = NO;
GCC_MODEL_CPU = G4;
GCC_OPTIMIZATION_LEVEL = 3;
- GCC_PREPROCESSOR_DEFINITIONS = (
- NDEBUG,
- REVISION_SUPPORT,
- );
+ GCC_PREPROCESSOR_DEFINITIONS = REVISION_SUPPORT;
GCC_UNROLL_LOOPS = YES;
HEADER_SEARCH_PATHS = source/event/;
INSTALL_PATH = "$(BUILT_PRODUCTS_DIR)/work";
- PRODUCT_NAME = primitive;
+ LIBRARY_SEARCH_PATHS = "";
+ PRODUCT_NAME = viewer;
SKIP_INSTALL = YES;
WARNING_CFLAGS = (
"-Wmost",
@@ -1912,26 +1881,27 @@
);
ZERO_LINK = NO;
};
- name = Deployment;
+ name = "Deployment-G5";
};
- 702442D50859E0B00059BD9B /* Profile */ = {
+ 70B393DF0944CA6F0018F09D /* Profile */ = {
isa = XCBuildConfiguration;
buildSettings = {
+ COPY_PHASE_STRIP = YES;
+ DEAD_CODE_STRIPPING = YES;
GCC_ALTIVEC_EXTENSIONS = YES;
GCC_AUTO_VECTORIZATION = YES;
GCC_DEBUGGING_SYMBOLS = full;
GCC_ENABLE_FIX_AND_CONTINUE = YES;
GCC_FAST_MATH = YES;
+ GCC_GENERATE_DEBUGGING_SYMBOLS = NO;
GCC_MODEL_CPU = G4;
GCC_OPTIMIZATION_LEVEL = 3;
- GCC_PREPROCESSOR_DEFINITIONS = (
- NDEBUG,
- REVISION_SUPPORT,
- );
+ GCC_PREPROCESSOR_DEFINITIONS = REVISION_SUPPORT;
GCC_UNROLL_LOOPS = YES;
HEADER_SEARCH_PATHS = source/event/;
INSTALL_PATH = "$(BUILT_PRODUCTS_DIR)/work";
- PRODUCT_NAME = primitive;
+ LIBRARY_SEARCH_PATHS = "";
+ PRODUCT_NAME = viewer;
SKIP_INSTALL = YES;
WARNING_CFLAGS = (
"-Wmost",
@@ -1942,39 +1912,48 @@
};
name = Profile;
};
- 702442D80859E0B00059BD9B /* Development */ = {
+ 70B393E00944CA6F0018F09D /* Deployment-G5 */ = {
isa = XCBuildConfiguration;
buildSettings = {
- GCC_OPTIMIZATION_LEVEL = 0;
- GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
- GCC_WARN_PEDANTIC = NO;
- };
- name = Development;
- };
- 702442D90859E0B00059BD9B /* Deployment */ = {
- isa = XCBuildConfiguration;
- buildSettings = {
- DEAD_CODE_STRIPPING = NO;
+ DEPLOYMENT_POSTPROCESSING = YES;
GCC_ALTIVEC_EXTENSIONS = YES;
GCC_AUTO_VECTORIZATION = YES;
GCC_DYNAMIC_NO_PIC = YES;
GCC_FAST_MATH = YES;
- GCC_GENERATE_DEBUGGING_SYMBOLS = NO;
+ GCC_MODEL_TUNING = G5;
GCC_OPTIMIZATION_LEVEL = 3;
+ GCC_PREPROCESSOR_DEFINITIONS = (
+ NDEBUG,
+ REVISION_SUPPORT,
+ );
GCC_UNROLL_LOOPS = YES;
+ WARNING_CFLAGS = (
+ "-Wmost",
+ "-Wno-four-char-constants",
+ "-Wno-unknown-pragmas",
+ );
};
- name = Deployment;
+ name = "Deployment-G5";
};
- 702442DA0859E0B00059BD9B /* Profile */ = {
+ 70B393E10944CA6F0018F09D /* Profile */ = {
isa = XCBuildConfiguration;
buildSettings = {
+ COPY_PHASE_STRIP = NO;
GCC_ALTIVEC_EXTENSIONS = YES;
GCC_AUTO_VECTORIZATION = YES;
+ GCC_DYNAMIC_NO_PIC = YES;
GCC_FAST_MATH = YES;
GCC_OPTIMIZATION_LEVEL = 3;
+ GCC_PREPROCESSOR_DEFINITIONS = (
+ NDEBUG,
+ REVISION_SUPPORT,
+ );
GCC_UNROLL_LOOPS = YES;
- GENERATE_PROFILING_CODE = YES;
- ZERO_LINK = NO;
+ WARNING_CFLAGS = (
+ "-Wmost",
+ "-Wno-four-char-constants",
+ "-Wno-unknown-pragmas",
+ );
};
name = Profile;
};
@@ -1985,31 +1964,34 @@
isa = XCConfigurationList;
buildConfigurations = (
700E2B7F085DE50C00CF158A /* Development */,
- 700E2B80085DE50C00CF158A /* Deployment */,
- 700E2B81085DE50C00CF158A /* Profile */,
+ 700E2B80085DE50C00CF158A /* Deployment-G4 */,
+ 70B393DE0944CA6F0018F09D /* Deployment-G5 */,
+ 70B393DF0944CA6F0018F09D /* Profile */,
);
defaultConfigurationIsVisible = 0;
- defaultConfigurationName = Deployment;
+ defaultConfigurationName = "Deployment-G4";
};
702442D20859E0B00059BD9B /* Build configuration list for PBXNativeTarget "primitive" */ = {
isa = XCConfigurationList;
buildConfigurations = (
702442D30859E0B00059BD9B /* Development */,
- 702442D40859E0B00059BD9B /* Deployment */,
- 702442D50859E0B00059BD9B /* Profile */,
+ 702442D40859E0B00059BD9B /* Deployment-G4 */,
+ 70B393DC0944CA6F0018F09D /* Deployment-G5 */,
+ 70B393DD0944CA6F0018F09D /* Profile */,
);
defaultConfigurationIsVisible = 0;
- defaultConfigurationName = Deployment;
+ defaultConfigurationName = "Deployment-G4";
};
702442D70859E0B00059BD9B /* Build configuration list for PBXProject "Avida" */ = {
isa = XCConfigurationList;
buildConfigurations = (
702442D80859E0B00059BD9B /* Development */,
- 702442D90859E0B00059BD9B /* Deployment */,
- 702442DA0859E0B00059BD9B /* Profile */,
+ 702442D90859E0B00059BD9B /* Deployment-G4 */,
+ 70B393E00944CA6F0018F09D /* Deployment-G5 */,
+ 70B393E10944CA6F0018F09D /* Profile */,
);
defaultConfigurationIsVisible = 0;
- defaultConfigurationName = Deployment;
+ defaultConfigurationName = "Deployment-G4";
};
/* End XCConfigurationList section */
};
Modified: development/source/analyze/cAnalyze.cc
===================================================================
--- development/source/analyze/cAnalyze.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/analyze/cAnalyze.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,18 +1,21 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cAnalyze.cc
+ * Avida
+ *
+ * Created by David on 12/1/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
+#include "cAnalyze.h"
+
#include <fstream>
#include <sstream>
#include <string>
#include <queue>
#include <stack>
-#include "cAnalyze.h"
-
#include "cAnalyzeCommand.h"
#include "cAnalyzeCommandDef.h"
#include "cAnalyzeCommandDefBase.h"
@@ -56,10 +59,6 @@
using namespace std;
-//////////////
-// cAnalyze
-//////////////
-
cAnalyze::cAnalyze(cWorld* world)
: cur_batch(0)
, m_world(world)
Modified: development/source/analyze/cAnalyze.h
===================================================================
--- development/source/analyze/cAnalyze.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/analyze/cAnalyze.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,32 +1,35 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cAnalyze.h
+ * Avida
+ *
+ * Created by David on 12/1/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef ANALYZE_HH
-#define ANALYZE_HH
+#ifndef cAnalyze_h
+#define cAnalyze_h
#include <vector>
-#ifndef GENOTYPE_BATCH_HH
+#ifndef cGenotypeBatch_h
#include "cGenotypeBatch.h"
#endif
#ifndef cRandom_h
#include "cRandom.h"
#endif
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
-#ifndef STRING_LIST_HH
+#ifndef cStringList_h
#include "cStringList.h"
#endif
-#ifndef TLIST_HH
+#ifndef tList_h
#include "tList.h"
#endif
-#define MAX_BATCHES 2000
+const int MAX_BATCHES = 2000;
namespace nAnalyze {
const int VERBOSE_SILENT = 0; // No output at all
Modified: development/source/analyze/cAnalyzeCommand.h
===================================================================
--- development/source/analyze/cAnalyzeCommand.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/analyze/cAnalyzeCommand.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,20 +1,22 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cAnalyzeCommand.h
+ * Avida
+ *
+ * Created by David on 12/1/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef ANALYZE_COMMAND_HH
-#define ANALYZE_COMMAND_HH
+#ifndef cAnalyzeCommand_h
+#define cAnalyzeCommand_h
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
// cAnalyzeCommand : A command in a loaded program
-class cString; // aggregate
template <class T> class tList;
class cAnalyzeCommand {
Modified: development/source/analyze/cAnalyzeCommandDef.h
===================================================================
--- development/source/analyze/cAnalyzeCommandDef.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/analyze/cAnalyzeCommandDef.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,22 +1,24 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cAnalyzeCommandDef.h
+ * Avida
+ *
+ * Created by David on 12/1/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef ANALYZE_COMMAND_DEF_HH
-#define ANALYZE_COMMAND_DEF_HH
+#ifndef cAnalyzeCommandDef_h
+#define cAnalyzeCommandDef_h
-#ifndef ANALYZE_COMMAND_DEF_BASE_HH
+#ifndef cAnalyzeCommandDefBase_h
#include "cAnalyzeCommandDefBase.h"
#endif
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
class cAnalyze;
-class cString; // aggregate
class cAnalyzeCommand;
class cAnalyzeCommandDef : public cAnalyzeCommandDefBase {
Modified: development/source/analyze/cAnalyzeCommandDefBase.h
===================================================================
--- development/source/analyze/cAnalyzeCommandDefBase.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/analyze/cAnalyzeCommandDefBase.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,18 +1,20 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cAnalyzeCommandDefBase.h
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef ANALYZE_COMMAND_DEF_BASE_HH
-#define ANALYZE_COMMAND_DEF_BASE_HH
+#ifndef cAnalyzeCommandDefBase_h
+#define cAnalyzeCommandDefBase_h
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
-class cString; // aggregate
class cAnalyze;
class cAnalyzeCommand;
Modified: development/source/analyze/cAnalyzeFlowCommand.h
===================================================================
--- development/source/analyze/cAnalyzeFlowCommand.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/analyze/cAnalyzeFlowCommand.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,23 +1,25 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cAnalyzeFlowCommand.h
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef ANALYZE_FLOW_COMMAND_HH
-#define ANALYZE_FLOW_COMMAND_HH
+#ifndef cAnalyzeFlowCommand_h
+#define cAnalyzeFlowCommand_h
-#ifndef ANALYZE_COMMAND_HH
+#ifndef cAnalyzeCommand_h
#include "cAnalyzeCommand.h"
#endif
-#ifndef TLIST_HH
+#ifndef tList_h
#include "tList.h"
#endif
// cAnalyzeFlowCommand : A cAnalyzeCommand containing other commands
-template <class T> class tList; // aggregate
class cString;
class cAnalyzeFlowCommand : public cAnalyzeCommand {
Modified: development/source/analyze/cAnalyzeFlowCommandDef.h
===================================================================
--- development/source/analyze/cAnalyzeFlowCommandDef.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/analyze/cAnalyzeFlowCommandDef.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,30 +1,30 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cAnalyzeFlowCommandDef.h
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef ANALYZE_FLOW_COMMAND_DEF_HH
-#define ANALYZE_FLOW_COMMAND_DEF_HH
+#ifndef cAnalyzeFlowCommandDef_h
+#define cAnalyzeFlowCommandDef_h
-#ifndef ANALYZE_COMMAND_HH
+#ifndef cAnalyzeCommand_h
#include "cAnalyzeCommand.h"
#endif
-#ifndef ANALYZE_COMMAND_DEF_BASE_HH
+#ifndef cAnalyzeCommandDefBase_h
#include "cAnalyzeCommandDefBase.h"
#endif
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
-#ifndef TLIST_HH
+#ifndef tList_h
#include "tList.h"
#endif
class cAnalyze;
-template <class T> class tList;
-class cAnalyzeCommand; // access
-class cString; // aggregate
class cAnalyzeFlowCommandDef : public cAnalyzeCommandDefBase {
private:
Modified: development/source/analyze/cAnalyzeFunction.h
===================================================================
--- development/source/analyze/cAnalyzeFunction.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/analyze/cAnalyzeFunction.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,29 +1,28 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cAnalyzeFunction.h
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef ANALYZE_FUNCTION_HH
-#define ANALYZE_FUNCTION_HH
+#ifndef cAnalyzeFunction_h
+#define cAnalyzeFunction_h
-#ifndef ANALYZE_COMMAND_HH
+#ifndef cAnalyzeCommand_h
#include "cAnalyzeCommand.h"
#endif
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
-#ifndef TLIST_HH
+#ifndef tList_h
#include "tList.h"
#endif
// cAnalyzeFunction : User-defined function
-class cString; // aggregate
-template <class T> class tList; // aggregate
-class cAnalyzeCommand;
-
class cAnalyzeFunction {
private:
cString name;
Modified: development/source/analyze/cAnalyzeGenotype.cc
===================================================================
--- development/source/analyze/cAnalyzeGenotype.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/analyze/cAnalyzeGenotype.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cAnalyzeGenotype.cc
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
#include "cAnalyzeGenotype.h"
@@ -19,10 +22,6 @@
using namespace std;
-//////////////////////
-// cAnalyzeGenotype
-//////////////////////
-
cAnalyzeGenotype::cAnalyzeGenotype(cWorld* world, cString symbol_string, cInstSet& in_inst_set)
: m_world(world)
, genome(symbol_string)
Modified: development/source/analyze/cAnalyzeGenotype.h
===================================================================
--- development/source/analyze/cAnalyzeGenotype.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/analyze/cAnalyzeGenotype.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,42 +1,40 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cAnalyzeGenotype.h
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef ANALYZE_GENOTYPE_HH
-#define ANALYZE_GENOTYPE_HH
+#ifndef cAnalyzeGenotype_h
+#define cAnalyzeGenotype_h
#include <fstream>
-#ifndef FUNCTIONS_HH
+#ifndef functions_h
#include "functions.h"
#endif
-#ifndef GENOME_HH
+#ifndef cGenome_h
#include "cGenome.h"
#endif
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
-#ifndef STRING_LIST_HH
+#ifndef cStringList_h
#include "cStringList.h"
#endif
-#ifndef STRING_UTIL_HH
+#ifndef cStringUtil_h
#include "cStringUtil.h"
#endif
-#ifndef TARRAY_HH
+#ifndef tArray_h
#include "tArray.h"
#endif
// cAnalyzeGenotype : Collection of information about loaded genotypes
-class cGenome; // aggregate
class cInstSet;
-class cString; // aggregate
-template <class T> class tArray; // aggregate
-class cStringList; // aggregate
-class cStringUtil; // access
class cWorld;
class cAnalyzeGenotype {
Modified: development/source/analyze/cAnalyzeUtil.cc
===================================================================
--- development/source/analyze/cAnalyzeUtil.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/analyze/cAnalyzeUtil.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2001 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cAnalyzeUtil.cc
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
#include "cAnalyzeUtil.h"
@@ -34,6 +37,7 @@
using namespace std;
+
void cAnalyzeUtil::TestGenome(cWorld* world, const cGenome & genome, cInstSet & inst_set,
ofstream& fp, int update)
{
Modified: development/source/analyze/cAnalyzeUtil.h
===================================================================
--- development/source/analyze/cAnalyzeUtil.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/analyze/cAnalyzeUtil.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,12 +1,15 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2001 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cAnalyzeUtil.h
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef ANALYZE_UTIL_HH
-#define ANALYZE_UTIL_HH
+#ifndef cAnalyzeUtil_h
+#define cAnalyzeUtil_h
#include <fstream>
Modified: development/source/analyze/cGenotypeBatch.h
===================================================================
--- development/source/analyze/cGenotypeBatch.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/analyze/cGenotypeBatch.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,24 +1,25 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cGenotypeBatch.h
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef GENOTYPE_BATCH_HH
-#define GENOTYPE_BATCH_HH
+#ifndef cGenotypeBatch_h
+#define cGenotypeBatch_h
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
-#ifndef TLIST_HH
+#ifndef tList_h
#include "tList.h"
#endif
// cGenotypeBatch : Collection of cAnalyzeGenotypes
-template <class T> class tList; // aggregate
-class cString; // aggregate
class cAnalyzeGenotype;
class cGenotypeBatch {
Modified: development/source/classification/CMakeLists.txt
===================================================================
--- development/source/classification/CMakeLists.txt 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/classification/CMakeLists.txt 2005-12-07 23:44:39 UTC (rev 414)
@@ -4,10 +4,8 @@
cClassificationManager.cc
cGenotype.cc
cGenotype_BirthData.cc
- cGenotype_TestData.cc
cGenotypeControl.cc
cInjectGenotype.cc
- cInjectGenotype_BirthData.cc
cInjectGenotypeControl.cc
cInjectGenotypeQueue.cc
cLineage.cc
Modified: development/source/classification/cGenotype.cc
===================================================================
--- development/source/classification/cGenotype.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/classification/cGenotype.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cGenotype.cc
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2003 California Institute of Technology.
+ *
+ */
#include "cGenotype.h"
@@ -18,12 +21,6 @@
using namespace std;
-class cSpecies;
-
-///////////////////////////
-// cGenotype
-///////////////////////////
-
cGenotype::cGenotype(cWorld* world, int in_update_born, int in_id)
: m_world(world)
, genome(1)
@@ -83,7 +80,7 @@
cInstruction temp_inst;
int inst_op;
fp >> inst_op;
- temp_inst.SetOp((UCHAR) inst_op);
+ temp_inst.SetOp((unsigned char) inst_op);
ret->genome[i] = temp_inst;
// @CAO add something here to load arguments for instructions.
}
@@ -112,6 +109,16 @@
return ret_value;
}
+void cGenotype::AddMerit(const cMerit & in)
+{
+ sum_merit.Add(in.GetDouble());
+}
+
+void cGenotype::RemoveMerit(const cMerit & in)
+{
+ sum_merit.Subtract(in.GetDouble());
+}
+
void cGenotype::SetParent(cGenotype * parent, cGenotype * parent2)
{
birth_data.parent_genotype = parent;
@@ -209,74 +216,6 @@
}
-bool cGenotype::GetTestViable() const {
- if (test_data.fitness == -1) CalcTestStats();
- return test_data.is_viable;
-}
-
-
-double cGenotype::GetTestFitness() const {
- if (test_data.fitness == -1) CalcTestStats();
- return test_data.fitness;
-}
-
-
-double cGenotype::GetTestMerit() const {
- if (test_data.fitness == -1) CalcTestStats();
- return test_data.merit;
-}
-
-
-int cGenotype::GetTestGestationTime() const {
- if (test_data.fitness == -1) CalcTestStats();
- return test_data.gestation_time;
-}
-
-
-int cGenotype::GetTestExecutedSize() const {
- if (test_data.fitness == -1) CalcTestStats();
- return test_data.executed_size;
-}
-
-
-int cGenotype::GetTestCopiedSize() const {
- if (test_data.fitness == -1) CalcTestStats();
- return test_data.copied_size;
-}
-
-
-double cGenotype::GetTestColonyFitness() const {
- if (test_data.fitness == -1) CalcTestStats();
- return test_data.colony_fitness;
-}
-
-
-int cGenotype::GetTestGenerations() const {
- if (test_data.fitness == -1) CalcTestStats();
- return test_data.generations;
-}
-
-void cGenotype::SetSpecies(cSpecies * in_species)
-{
- species = in_species;
-}
-
-void cGenotype::AddMerit(const cMerit & in)
-{
- sum_merit.Add(in.GetDouble());
-}
-
-void cGenotype::RemoveMerit(const cMerit & in)
-{
- sum_merit.Subtract(in.GetDouble());
-}
-
-void cGenotype::Deactivate(int update)
-{
- is_active = false;
- birth_data.update_deactivated = update;
-}
-
int cGenotype::GetPhyloDistance(cGenotype * test_genotype)
{
if (GetID() == test_genotype->GetID()) {
@@ -346,17 +285,3 @@
return 5;
}
-
-
-int cGenotype::AddOrganism()
-{
- total_organisms++;
- return num_organisms++;
-}
-
-int cGenotype::RemoveOrganism()
-{
- birth_data.death_track.Inc();
- return num_organisms--;
-}
-
Modified: development/source/classification/cGenotype.h
===================================================================
--- development/source/classification/cGenotype.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/classification/cGenotype.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,28 +1,31 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cGenotype.h
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2003 California Institute of Technology.
+ *
+ */
-#ifndef GENOTYPE_HH
-#define GENOTYPE_HH
+#ifndef cGenotype_h
+#define cGenotype_h
#include <fstream>
-#ifndef DOUBLE_SUM_HH
+#ifndef cDoubleSum_h
#include "cDoubleSum.h"
#endif
-#ifndef GENOME_HH
+#ifndef cGenome_h
#include "cGenome.h"
#endif
-#ifndef GENOTYPE_BIRTH_DATA_HH
+#ifndef cGenotype_BirthData_h
#include "cGenotype_BirthData.h"
#endif
-#ifndef GENOTYPE_TEST_DATA_HH
+#ifndef cGenotype_TestData_h
#include "cGenotype_TestData.h"
#endif
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
@@ -54,7 +57,7 @@
int total_organisms;
int total_parasites;
- cSpecies * species;
+ cSpecies* species;
// Data Structure stuff...
cGenotype * next;
@@ -100,17 +103,17 @@
void UpdateReset();
void SetGenome(const cGenome & in_genome);
- void SetSpecies(cSpecies * in_species);
+ void SetSpecies(cSpecies * in_species) { species = in_species; }
// Test CPU info -- only used with limited options on.
- bool GetTestViable() const;
- double GetTestFitness() const;
- double GetTestMerit() const;
- int GetTestGestationTime() const;
- int GetTestExecutedSize() const;
- int GetTestCopiedSize() const;
- double GetTestColonyFitness() const;
- int GetTestGenerations() const;
+ inline bool GetTestViable() const;
+ inline double GetTestFitness() const;
+ inline double GetTestMerit() const;
+ inline int GetTestGestationTime() const;
+ inline int GetTestExecutedSize() const;
+ inline int GetTestCopiedSize() const;
+ inline double GetTestColonyFitness() const;
+ inline int GetTestGenerations() const;
void SetParent(cGenotype * parent, cGenotype * parent2);
void SetName(cString in_name) { name = in_name; }
@@ -209,32 +212,33 @@
// and grand-parents, including sexual tracking.
int GetPhyloDistance(cGenotype * test_genotype);
- int AddOrganism();
- int RemoveOrganism();
- int AddParasite() { return ++total_parasites; }
- void SwapOrganism() { total_organisms++; }
- int GetNumOrganisms() { return num_organisms; }
- int GetTotalOrganisms() { return total_organisms; }
- int GetTotalParasites() { return total_parasites; }
+ inline int AddOrganism();
+ inline int RemoveOrganism();
+ int AddParasite() { return ++total_parasites; }
+ void SwapOrganism() { total_organisms++; }
+ int GetNumOrganisms() { return num_organisms; }
+ int GetTotalOrganisms() { return total_organisms; }
+ int GetTotalParasites() { return total_parasites; }
};
-// The genotype pointer template...
+inline int cGenotype::AddOrganism()
+{
+ total_organisms++;
+ return num_organisms++;
+}
+inline int cGenotype::RemoveOrganism()
+{
+ birth_data.death_track.Inc();
+ return num_organisms--;
+}
-
-// All the inline stuff...
-
- ////////////////
- // cGenotype //
-////////////////
-
inline void cGenotype::SetThreshold()
{
flag_threshold = true;
if (symbol == '.') symbol = '+';
}
-
inline void cGenotype::SetBreedStats(cGenotype & daughter)
{
birth_data.birth_track.Inc();
@@ -246,4 +250,58 @@
}
}
+inline bool cGenotype::GetTestViable() const {
+ if (test_data.fitness == -1) CalcTestStats();
+ return test_data.is_viable;
+}
+
+
+inline double cGenotype::GetTestFitness() const {
+ if (test_data.fitness == -1) CalcTestStats();
+ return test_data.fitness;
+}
+
+
+inline double cGenotype::GetTestMerit() const {
+ if (test_data.fitness == -1) CalcTestStats();
+ return test_data.merit;
+}
+
+
+inline int cGenotype::GetTestGestationTime() const {
+ if (test_data.fitness == -1) CalcTestStats();
+ return test_data.gestation_time;
+}
+
+
+inline int cGenotype::GetTestExecutedSize() const {
+ if (test_data.fitness == -1) CalcTestStats();
+ return test_data.executed_size;
+}
+
+
+inline int cGenotype::GetTestCopiedSize() const {
+ if (test_data.fitness == -1) CalcTestStats();
+ return test_data.copied_size;
+}
+
+
+inline double cGenotype::GetTestColonyFitness() const {
+ if (test_data.fitness == -1) CalcTestStats();
+ return test_data.colony_fitness;
+}
+
+
+inline int cGenotype::GetTestGenerations() const {
+ if (test_data.fitness == -1) CalcTestStats();
+ return test_data.generations;
+}
+
+inline void cGenotype::Deactivate(int update)
+{
+ is_active = false;
+ birth_data.update_deactivated = update;
+}
+
+
#endif
Modified: development/source/classification/cGenotypeControl.cc
===================================================================
--- development/source/classification/cGenotypeControl.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/classification/cGenotypeControl.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cGenotypeControl.cc
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2003 California Institute of Technology.
+ *
+ */
#include "cGenotypeControl.h"
Modified: development/source/classification/cGenotypeControl.h
===================================================================
--- development/source/classification/cGenotypeControl.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/classification/cGenotypeControl.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cGenotypeControl.h
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2003 California Institute of Technology.
+ *
+ */
#ifndef cGenotypeControl_h
#define cGenotypeControl_h
Modified: development/source/classification/cGenotype_BirthData.cc
===================================================================
--- development/source/classification/cGenotype_BirthData.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/classification/cGenotype_BirthData.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,21 +1,17 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cGenotype_BirthData.cc
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2003 California Institute of Technology.
+ *
+ */
-#ifndef GENOTYPE_BIRTH_DATA_HH
#include "cGenotype_BirthData.h"
-#endif
-#ifndef DEFS_HH
#include "defs.h"
-#endif
-/////////////////////////
-// cGenotype_BirthData
-/////////////////////////
cGenotype_BirthData::cGenotype_BirthData(int in_update_born)
: update_born(in_update_born)
@@ -31,7 +27,3 @@
ancestor_ids.Resize(6);
ancestor_ids.SetAll(-1);
}
-
-cGenotype_BirthData::~cGenotype_BirthData()
-{
-}
Modified: development/source/classification/cGenotype_BirthData.h
===================================================================
--- development/source/classification/cGenotype_BirthData.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/classification/cGenotype_BirthData.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,27 +1,30 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cGenotype_BirthData.h
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2003 California Institute of Technology.
+ *
+ */
-#ifndef GENOTYPE_BIRTH_DATA_HH
-#define GENOTYPE_BIRTH_DATA_HH
+#ifndef cGenotype_BirthData_h
+#define cGenotype_BirthData_h
-#ifndef COUNT_TRACKER_HH
+#ifndef cCountTracker_h
#include "cCountTracker.h"
#endif
-
-#ifndef TARRAY_HH
+#ifndef tArray_h
#include "tArray.h"
#endif
class cGenotype;
class cSpecies;
+
class cGenotype_BirthData {
public:
cGenotype_BirthData(int in_update_born);
- ~cGenotype_BirthData();
+ ~cGenotype_BirthData() { ; }
cCountTracker birth_track;
cCountTracker death_track;
Deleted: development/source/classification/cGenotype_TestData.cc
===================================================================
--- development/source/classification/cGenotype_TestData.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/classification/cGenotype_TestData.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,23 +0,0 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
-
-#ifndef GENOTYPE_TEST_DATA_HH
-#include "cGenotype_TestData.h"
-#endif
-
-////////////////////////
-// cGenotype_TestData
-////////////////////////
-
-cGenotype_TestData::cGenotype_TestData()
- : fitness(-1)
-{
-}
-
-cGenotype_TestData::~cGenotype_TestData()
-{
-}
Modified: development/source/classification/cGenotype_TestData.h
===================================================================
--- development/source/classification/cGenotype_TestData.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/classification/cGenotype_TestData.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,17 +1,20 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cGenotype_TestData.h
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2003 California Institute of Technology.
+ *
+ */
-#ifndef GENOTYPE_TEST_DATA_HH
-#define GENOTYPE_TEST_DATA_HH
+#ifndef cGenotype_TestData_h
+#define cGenotype_TestData_h
class cGenotype_TestData {
public:
- cGenotype_TestData();
- ~cGenotype_TestData();
+ cGenotype_TestData() : fitness(-1) { ; }
+ ~cGenotype_TestData() { ; }
bool is_viable;
Modified: development/source/classification/cInjectGenotype.cc
===================================================================
--- development/source/classification/cInjectGenotype.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/classification/cInjectGenotype.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -70,7 +70,7 @@
cInstruction temp_inst;
int inst_op;
fp >> inst_op;
- temp_inst.SetOp((UCHAR) inst_op);
+ temp_inst.SetOp((unsigned char) inst_op);
genome[i] = temp_inst;
// @CAO add something here to load arguments for instructions.
}
Modified: development/source/classification/cInjectGenotypeElement.h
===================================================================
--- development/source/classification/cInjectGenotypeElement.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/classification/cInjectGenotypeElement.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,35 +1,38 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cInjectGenotypeElement.h
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef INJECT_GENOTYPE_ELEMENT_HH
-#define INJECT_GENOTYPE_ELEMENT_HH
+#ifndef cInjectGenotypeElement_h
+#define cInjectGenotypeElement_h
-#ifndef DEFS_HH
+#ifndef defs_h
#include "defs.h"
#endif
class cInjectGenotype;
+
class cInjectGenotypeElement {
private:
- cInjectGenotype * inject_genotype;
- cInjectGenotypeElement * next;
- cInjectGenotypeElement * prev;
+ cInjectGenotype* inject_genotype;
+ cInjectGenotypeElement* next;
+ cInjectGenotypeElement* prev;
public:
- inline cInjectGenotypeElement(cInjectGenotype * in_gen=NULL) : inject_genotype(in_gen) {
- next = NULL; prev = NULL;
- }
- inline ~cInjectGenotypeElement() { ; }
+ cInjectGenotypeElement(cInjectGenotype* in_gen = NULL)
+ : inject_genotype(in_gen), next(NULL), prev(NULL) { ; }
+ ~cInjectGenotypeElement() { ; }
- inline cInjectGenotype * GetInjectGenotype() const { return inject_genotype; }
- inline cInjectGenotypeElement * GetNext() const { return next; }
- inline cInjectGenotypeElement * GetPrev() const { return prev; }
+ cInjectGenotype* GetInjectGenotype() const { return inject_genotype; }
+ cInjectGenotypeElement* GetNext() const { return next; }
+ cInjectGenotypeElement* GetPrev() const { return prev; }
- inline void SetNext(cInjectGenotypeElement * in_next) { next = in_next; }
- inline void SetPrev(cInjectGenotypeElement * in_prev) { prev = in_prev; }
+ void SetNext(cInjectGenotypeElement* in_next) { next = in_next; }
+ void SetPrev(cInjectGenotypeElement* in_prev) { prev = in_prev; }
};
#endif
Modified: development/source/classification/cInjectGenotypeQueue.cc
===================================================================
--- development/source/classification/cInjectGenotypeQueue.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/classification/cInjectGenotypeQueue.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,23 +1,19 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cInjectGenotypeQueue.cc
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef INJECT_GENOTYPE_QUEUE_HH
#include "cInjectGenotypeQueue.h"
-#endif
-#ifndef INJECT_GENOTYPE_HH
#include "cInjectGenotype.h"
-#endif
#include <assert.h>
-/////////////////////
-// cInjectGenotypeQueue
-/////////////////////
cInjectGenotypeQueue::cInjectGenotypeQueue()
{
Modified: development/source/classification/cInjectGenotypeQueue.h
===================================================================
--- development/source/classification/cInjectGenotypeQueue.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/classification/cInjectGenotypeQueue.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,25 +1,29 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cInjectGenotypeQueue.h
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef INJECT_GENOTYPE_QUEUE_HH
-#define INJECT_GENOTYPE_QUEUE_HH
+#ifndef cInjectGenotypeQueue_h
+#define cInjectGenotypeQueue_h
-#ifndef INJECT_GENOTYPE_ELEMENT_HH
+#ifndef cInjectGenotypeElement_h
#include "cInjectGenotypeElement.h"
#endif
class cInjectGenotype;
class cGenome;
+
class cInjectGenotypeQueue {
private:
int size;
cInjectGenotypeElement root;
- void Remove(cInjectGenotypeElement * in_element);
+ void Remove(cInjectGenotypeElement* in_element);
public:
cInjectGenotypeQueue();
~cInjectGenotypeQueue();
Deleted: development/source/classification/cInjectGenotype_BirthData.cc
===================================================================
--- development/source/classification/cInjectGenotype_BirthData.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/classification/cInjectGenotype_BirthData.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,32 +0,0 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
-
-#ifndef INJECT_GENOTYPE_BIRTH_DATA_HH
-#include "cInjectGenotype_BirthData.h"
-#endif
-
-#ifndef DEFS_HH
-#include "defs.h"
-#endif
-
-/////////////////////////
-// cInjectGenotype_BirthData
-/////////////////////////
-
-cInjectGenotype_BirthData::cInjectGenotype_BirthData(int in_update_born)
- : update_born(in_update_born)
- , parent_id(-1)
- , gene_depth(0)
- , update_deactivated(-1)
- , parent_genotype(NULL)
- , num_offspring_genotypes(0)
-{
-}
-
-cInjectGenotype_BirthData::~cInjectGenotype_BirthData()
-{
-}
Modified: development/source/classification/cInjectGenotype_BirthData.h
===================================================================
--- development/source/classification/cInjectGenotype_BirthData.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/classification/cInjectGenotype_BirthData.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,22 +1,26 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cInjectGenotype_BirthData.h
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2003 California Institute of Technology.
+ *
+ */
-#ifndef INJECT_GENOTYPE_BIRTH_DATA_HH
-#define INJECT_GENOTYPE_BIRTH_DATA_HH
+#ifndef cInjectGenotype_BirthData_h
+#define cInjectGenotype_BirthData_h
-#ifndef COUNT_TRACKER_HH
+#ifndef cCountTracker_h
#include "cCountTracker.h"
#endif
class cInjectGenotype;
+
class cInjectGenotype_BirthData {
public:
- cInjectGenotype_BirthData(int in_update_born);
- ~cInjectGenotype_BirthData();
+ inline cInjectGenotype_BirthData(int in_update_born);
+ ~cInjectGenotype_BirthData() { ; }
cCountTracker birth_track;
cCountTracker death_track;
@@ -35,4 +39,14 @@
int num_offspring_genotypes; // Num offspring genotypes still in memory.
};
+inline cInjectGenotype_BirthData::cInjectGenotype_BirthData(int in_update_born)
+: update_born(in_update_born)
+, parent_id(-1)
+, gene_depth(0)
+, update_deactivated(-1)
+, parent_genotype(NULL)
+, num_offspring_genotypes(0)
+{
+}
+
#endif
Modified: development/source/classification/cLineage.cc
===================================================================
--- development/source/classification/cLineage.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/classification/cLineage.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,16 +1,16 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2001 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cLineage.cc
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2001 California Institute of Technology.
+ *
+ */
-#ifndef LINEAGE_HH
#include "cLineage.h"
-#endif
-#ifndef GENOTYPE_HH
+
#include "cGenotype.h"
-#endif
using namespace std;
Modified: development/source/classification/cLineage.h
===================================================================
--- development/source/classification/cLineage.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/classification/cLineage.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,12 +1,15 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2001 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cLineage.h
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2001 California Institute of Technology.
+ *
+ */
-#ifndef LINEAGE_HH
-#define LINEAGE_HH
+#ifndef cLineage_h
+#define cLineage_h
#include <map>
Modified: development/source/classification/cSpecies.cc
===================================================================
--- development/source/classification/cSpecies.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/classification/cSpecies.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2001 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cSpecies.cc
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2001 California Institute of Technology.
+ *
+ */
#include "cSpecies.h"
@@ -29,13 +32,13 @@
total_organisms = 0;
total_genotypes = 0;
- queue_type = SPECIES_QUEUE_NONE;
+ queue_type = nSpecies::QUEUE_NONE;
next = NULL;
prev = NULL;
// Track distance of each genome as it is passed in...
- for (int i = 0; i < SPECIES_MAX_DISTANCE; i++) {
+ for (int i = 0; i < nSpecies::MAX_DISTANCE; i++) {
genotype_distance[i] = 0;
}
}
@@ -43,7 +46,7 @@
cSpecies::~cSpecies()
{
int i, total_count = 0;
- for (i = 0; i < SPECIES_MAX_DISTANCE; i++) {
+ for (i = 0; i < nSpecies::MAX_DISTANCE; i++) {
total_count += genotype_distance[i];
}
@@ -54,7 +57,7 @@
FILE * fp = stats.GetTestFP();
fprintf(fp, "Species %3d: ", id_num);
- for (i = 0; i < SPECIES_MAX_DISTANCE; i++) {
+ for (i = 0; i < nSpecies::MAX_DISTANCE; i++) {
fprintf(fp, "%2d ", genotype_distance[i]);
}
fprintf(fp, "\n");
@@ -148,7 +151,7 @@
const int distance =
cGenomeUtil::FindEditDistance(genome, in_genotype.GetGenome());
- if (distance >= 0 && distance < SPECIES_MAX_DISTANCE)
+ if (distance >= 0 && distance < nSpecies::MAX_DISTANCE)
genotype_distance[distance]++;
num_threshold++;
Modified: development/source/classification/cSpecies.h
===================================================================
--- development/source/classification/cSpecies.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/classification/cSpecies.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,26 +1,25 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2001 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cSpecies.h
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2001 California Institute of Technology.
+ *
+ */
-#ifndef SPECIES_HH
-#define SPECIES_HH
+#ifndef cSpecies_h
+#define cSpecies_h
#include <fstream>
-#ifndef GENOME_HH
+#ifndef cGenome_h
#include "cGenome.h"
#endif
+#ifndef nSpecies_h
+#include "nSpecies.h"
+#endif
-#define SPECIES_QUEUE_NONE 0
-#define SPECIES_QUEUE_ACTIVE 1
-#define SPECIES_QUEUE_INACTIVE 2
-#define SPECIES_QUEUE_GARBAGE 3
-
-#define SPECIES_MAX_DISTANCE 20
-
class cGenotype;
class cWorld;
@@ -41,7 +40,7 @@
int num_organisms;
int queue_type;
char symbol;
- int genotype_distance[SPECIES_MAX_DISTANCE];
+ int genotype_distance[nSpecies::MAX_DISTANCE];
cSpecies * next;
cSpecies * prev;
Modified: development/source/classification/cSpeciesControl.cc
===================================================================
--- development/source/classification/cSpeciesControl.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/classification/cSpeciesControl.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cSpeciesControl.cc
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
#include "cSpeciesControl.h"
@@ -16,38 +19,30 @@
#include <assert.h>
-cSpeciesControl::cSpeciesControl(cWorld* world) : m_world(world)
-{
-}
-
-cSpeciesControl::~cSpeciesControl()
-{
-}
-
void cSpeciesControl::Remove(cSpecies & in_species)
{
switch (in_species.GetQueueType()) {
- case SPECIES_QUEUE_ACTIVE:
+ case nSpecies::QUEUE_ACTIVE:
active_queue.Remove(in_species);
break;
- case SPECIES_QUEUE_INACTIVE:
+ case nSpecies::QUEUE_INACTIVE:
inactive_queue.Remove(in_species);
break;
- case SPECIES_QUEUE_GARBAGE:
+ case nSpecies::QUEUE_GARBAGE:
garbage_queue.Remove(in_species);
break;
default:
break;
}
- in_species.SetQueueType(SPECIES_QUEUE_NONE);
+ in_species.SetQueueType(nSpecies::QUEUE_NONE);
}
void cSpeciesControl::Adjust(cSpecies & in_species)
{
// Only adjust if this species is in the active queue.
- if (in_species.GetQueueType() == SPECIES_QUEUE_ACTIVE) {
+ if (in_species.GetQueueType() == nSpecies::QUEUE_ACTIVE) {
active_queue.Adjust(in_species);
}
}
@@ -56,21 +51,21 @@
{
Remove(in_species);
active_queue.InsertRear(in_species);
- in_species.SetQueueType(SPECIES_QUEUE_ACTIVE);
+ in_species.SetQueueType(nSpecies::QUEUE_ACTIVE);
}
void cSpeciesControl::SetInactive(cSpecies & in_species)
{
Remove(in_species);
inactive_queue.InsertRear(in_species);
- in_species.SetQueueType(SPECIES_QUEUE_INACTIVE);
+ in_species.SetQueueType(nSpecies::QUEUE_INACTIVE);
}
void cSpeciesControl::SetGarbage(cSpecies & in_species)
{
Remove(in_species);
garbage_queue.InsertRear(in_species);
- in_species.SetQueueType(SPECIES_QUEUE_GARBAGE);
+ in_species.SetQueueType(nSpecies::QUEUE_GARBAGE);
}
bool cSpeciesControl::OK()
@@ -79,9 +74,9 @@
// Check the queues.
- assert (active_queue.OK(SPECIES_QUEUE_ACTIVE));
- assert (inactive_queue.OK(SPECIES_QUEUE_INACTIVE));
- assert (garbage_queue.OK(SPECIES_QUEUE_GARBAGE));
+ assert (active_queue.OK(nSpecies::QUEUE_ACTIVE));
+ assert (inactive_queue.OK(nSpecies::QUEUE_INACTIVE));
+ assert (garbage_queue.OK(nSpecies::QUEUE_GARBAGE));
return ret_value;
}
Modified: development/source/classification/cSpeciesControl.h
===================================================================
--- development/source/classification/cSpeciesControl.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/classification/cSpeciesControl.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,14 +1,17 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cSpeciesControl.h
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef SPECIES_CONTROL_HH
-#define SPECIES_CONTROL_HH
+#ifndef cSpeciesControl_h
+#define cSpeciesControl_h
-#ifndef SPECIES_QUEUE_HH
+#ifndef cSpeciesQueue_h
#include "cSpeciesQueue.h"
#endif
@@ -25,8 +28,8 @@
cSpeciesQueue garbage_queue;
public:
- cSpeciesControl(cWorld* world);
- ~cSpeciesControl();
+ cSpeciesControl(cWorld* world) : m_world(world) { ; }
+ ~cSpeciesControl() { ; }
void Remove(cSpecies & in_species);
void Adjust(cSpecies & in_species);
Modified: development/source/classification/cSpeciesQueue.cc
===================================================================
--- development/source/classification/cSpeciesQueue.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/classification/cSpeciesQueue.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,35 +1,19 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cSpeciesQueue.cc
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef SPECIES_QUEUE_HH
#include "cSpeciesQueue.h"
-#endif
-#ifndef DEFS_HH
#include "defs.h"
-#endif
-#ifndef SPECIES_HH
#include "cSpecies.h"
-#endif
-///////////////////
-// cSpeciesQueue
-///////////////////
-cSpeciesQueue::cSpeciesQueue()
-{
- size = 0;
- first = NULL;
-}
-
-cSpeciesQueue::~cSpeciesQueue()
-{
-}
-
void cSpeciesQueue::InsertRear(cSpecies & new_species)
{
// If the queue doesn't exist, create it with this species as the only
Modified: development/source/classification/cSpeciesQueue.h
===================================================================
--- development/source/classification/cSpeciesQueue.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/classification/cSpeciesQueue.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,21 +1,29 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cSpeciesQueue.h
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef SPECIES_QUEUE_HH
-#define SPECIES_QUEUE_HH
+#ifndef cSpeciesQueue_h
+#define cSpeciesQueue_h
+#ifndef defs_h
+#include "defs.h"
+#endif
+
class cSpecies;
+
class cSpeciesQueue {
private:
int size;
- cSpecies * first;
+ cSpecies* first;
public:
- cSpeciesQueue();
- ~cSpeciesQueue();
+ cSpeciesQueue() : size(0), first(NULL) { ; }
+ ~cSpeciesQueue() { ; }
void InsertRear(cSpecies & new_species);
void Remove(cSpecies & in_species);
Modified: development/source/classification/nSpecies.h
===================================================================
--- development/source/classification/nSpecies.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/classification/nSpecies.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -12,6 +12,8 @@
namespace nSpecies {
enum tRecording { RECORD_OFF = 0, RECORD_FULL = 1, RECORD_LIMITED = 2 };
+ enum { QUEUE_NONE = 0, QUEUE_ACTIVE, QUEUE_INACTIVE, QUEUE_GARBAGE };
+ static const int MAX_DISTANCE = 20;
}
#endif
Modified: development/source/cpu/cCPUMemory.cc
===================================================================
--- development/source/cpu/cCPUMemory.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cCPUMemory.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,23 +1,20 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cCPUMemory.cc
+ * Avida
+ *
+ * Created by David on 11/22/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef CPU_MEMORY_HH
#include "cCPUMemory.h"
-#endif
using namespace std;
const double MEMORY_INCREASE_FACTOR = 1.5;
const double MEMORY_SHRINK_TEST_FACTOR = 4.0;
-////////////////
-// cCPUMemory
-////////////////
-
cCPUMemory::cCPUMemory(int _size) : cGenome(_size), flag_array(_size)
{
}
Modified: development/source/cpu/cCPUMemory.h
===================================================================
--- development/source/cpu/cCPUMemory.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cCPUMemory.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,20 +1,23 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cCPUMemory.h
+ * Avida
+ *
+ * Created by David on 11/22/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef CPU_MEMORY_HH
-#define CPU_MEMORY_HH
+#ifndef cCPUMemory_h
+#define cCPUMemory_h
-#ifndef GENOME_HH
+#ifndef cGenome_h
#include "cGenome.h"
#endif
-#ifndef TARRAY_HH
+#ifndef tArray_h
#include "tArray.h"
#endif
-#ifndef MEMORY_FLAGS_HH
+#ifndef cMemoryFlags_h
#include "cMemoryFlags.h"
#endif
Modified: development/source/cpu/cCPUTestInfo.cc
===================================================================
--- development/source/cpu/cCPUTestInfo.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cCPUTestInfo.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cCPUTestInfo.h
+ * Avida
+ *
+ * Created by David on 11/29/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2003 California Institute of Technology.
+ *
+ */
#include "cCPUTestInfo.h"
@@ -13,10 +16,6 @@
#include <assert.h>
-/////////////////
-// cCPUTestInfo
-/////////////////
-
cCPUTestInfo::cCPUTestInfo(int max_tests)
: generation_tests(max_tests) // These vars not reset on Clear()
, test_threads(false)
Modified: development/source/cpu/cCPUTestInfo.h
===================================================================
--- development/source/cpu/cCPUTestInfo.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cCPUTestInfo.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,20 +1,23 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cCPUTestInfo.h
+ * Avida
+ *
+ * Created by David on 11/29/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2003 California Institute of Technology.
+ *
+ */
-#ifndef CPU_TEST_INFO_HH
-#define CPU_TEST_INFO_HH
+#ifndef cCPUTestInfo_h
+#define cCPUTestInfo_h
#ifndef nHardware_h
#include "nHardware.h"
#endif
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
-#ifndef TARRAY_HH
+#ifndef tArray_h
#include "tArray.h"
#endif
Modified: development/source/cpu/cCodeLabel.cc
===================================================================
--- development/source/cpu/cCodeLabel.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cCodeLabel.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,17 +1,18 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2002 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cCodeLabel.cc
+ * Avida
+ *
+ * Created by David on 11/22/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
#include "cCodeLabel.h"
-#include "cTools.h" // for g_memory & g_debug
-
+#include "cTools.h"
#include "nHardwareCPU.h"
-
#include <cmath>
#include <vector>
#include <iostream>
@@ -19,12 +20,6 @@
using namespace std;
-
-
-////////////////////////////////
-// cCodeLabel stuff...
-////////////////////////////////
-
bool cCodeLabel::OK()
{
bool result = true;
Modified: development/source/cpu/cCodeLabel.h
===================================================================
--- development/source/cpu/cCodeLabel.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cCodeLabel.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,26 +1,29 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cCodeLabel.h
+ * Avida
+ *
+ * Created by David on 11/22/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef CODE_LABEL_HH
-#define CODE_LABEL_HH
+#ifndef cCodeLabel_h
+#define cCodeLabel_h
#ifndef nHardware_h
-#include "nHardware.h" // #defines only
+#include "nHardware.h"
#endif
-#ifndef DEFS_HH
+#ifndef defs_h
#include "defs.h"
#endif
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
-#ifndef TARRAY_HH
+#ifndef tArray_h
#include "tArray.h"
#endif
-#ifndef TOOLS_HH
+#ifndef cTools_h
#include "cTools.h"
#endif
Modified: development/source/cpu/cHardware4Stack.cc
===================================================================
--- development/source/cpu/cHardware4Stack.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cHardware4Stack.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1328,21 +1328,21 @@
// Divide Mutations
if (organism->TestDivideMut()) {
- const UINT mut_line = m_world->GetRandom().GetUInt(child_genome.GetSize());
+ const unsigned int mut_line = m_world->GetRandom().GetUInt(child_genome.GetSize());
child_genome[mut_line] = m_inst_set->GetRandomInst();
cpu_stats.mut_stats.divide_mut_count++;
}
// Divide Insertions
if (organism->TestDivideIns() && child_genome.GetSize() < MAX_CREATURE_SIZE){
- const UINT mut_line = m_world->GetRandom().GetUInt(child_genome.GetSize() + 1);
+ const unsigned int mut_line = m_world->GetRandom().GetUInt(child_genome.GetSize() + 1);
child_genome.Insert(mut_line, m_inst_set->GetRandomInst());
cpu_stats.mut_stats.divide_insert_mut_count++;
}
// Divide Deletions
if (organism->TestDivideDel() && child_genome.GetSize() > MIN_CREATURE_SIZE){
- const UINT mut_line = m_world->GetRandom().GetUInt(child_genome.GetSize());
+ const unsigned int mut_line = m_world->GetRandom().GetUInt(child_genome.GetSize());
// if( child_genome.FlagCopied(mut_line) == true) copied_size_change--;
child_genome.Remove(mut_line);
cpu_stats.mut_stats.divide_delete_mut_count++;
@@ -1440,21 +1440,21 @@
// Divide Mutations
if (organism->TestDivideMut()) {
- const UINT mut_line = m_world->GetRandom().GetUInt(injected_code.GetSize());
+ const unsigned int mut_line = m_world->GetRandom().GetUInt(injected_code.GetSize());
injected_code[mut_line] = m_inst_set->GetRandomInst();
//cpu_stats.mut_stats.divide_mut_count++;
}
// Divide Insertions
if (organism->TestDivideIns() && injected_code.GetSize() < MAX_CREATURE_SIZE){
- const UINT mut_line = m_world->GetRandom().GetUInt(injected_code.GetSize() + 1);
+ const unsigned int mut_line = m_world->GetRandom().GetUInt(injected_code.GetSize() + 1);
injected_code.Insert(mut_line, m_inst_set->GetRandomInst());
//cpu_stats.mut_stats.divide_insert_mut_count++;
}
// Divide Deletions
if (organism->TestDivideDel() && injected_code.GetSize() > MIN_CREATURE_SIZE){
- const UINT mut_line = m_world->GetRandom().GetUInt(injected_code.GetSize());
+ const unsigned int mut_line = m_world->GetRandom().GetUInt(injected_code.GetSize());
// if( injected_code.FlagCopied(mut_line) == true) copied_size_change--;
injected_code.Remove(mut_line);
//cpu_stats.mut_stats.divide_delete_mut_count++;
Modified: development/source/cpu/cHardware4Stack_Thread.cc
===================================================================
--- development/source/cpu/cHardware4Stack_Thread.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cHardware4Stack_Thread.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,20 +1,17 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cHardware4Stack_Thread.cc
+ * Avida
+ *
+ * Created by David on 11/17/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2003 California Institute of Technology.
+ *
+ */
-#ifndef HARDWARE_4STACK_THREAD_HH
#include "cHardware4Stack_Thread.h"
-#endif
using namespace std;
-/////////////////////////
-// cHardware4Stack_Thread
-/////////////////////////
-
cHardware4Stack_Thread::cHardware4Stack_Thread(cHardwareBase * in_hardware, int _id)
{
Reset(in_hardware, _id);
Modified: development/source/cpu/cHardware4Stack_Thread.h
===================================================================
--- development/source/cpu/cHardware4Stack_Thread.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cHardware4Stack_Thread.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,28 +1,31 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cHardware4Stack_Thread.h
+ * Avida
+ *
+ * Created by David on 11/17/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2003 California Institute of Technology.
+ *
+ */
-#ifndef HARDWARE_4STACK_THREAD_HH
-#define HARDWARE_4STACK_THREAD_HH
+#ifndef cHardware4Stack_Thread_h
+#define cHardware4Stack_Thread_h
#include <iostream>
-#ifndef CODE_LABEL_HH
+#ifndef cCodeLabel_h
#include "cCodeLabel.h"
#endif
-#ifndef CPU_STACK_HH
+#ifndef cCPUStack_h
#include "cCPUStack.h"
#endif
-#ifndef HEAD_MULTI_MEM_HH
+#ifndef cHeadMulitMem_h
#include "cHeadMultiMem.h"
#endif
-#ifndef HARDWARE_4STACK_CONSTANTS_HH
+#ifndef nHardware4Stack_h
#include "nHardware4Stack.h"
#endif
-#ifndef TBUFFER_HH
+#ifndef tBuffer_h
#include "tBuffer.h"
#endif
@@ -44,7 +47,7 @@
int id;
public:
cHeadMultiMem heads[nHardware::NUM_HEADS];
- UCHAR cur_head;
+ unsigned char cur_head;
cCPUStack local_stacks[nHardware4Stack::NUM_LOCAL_STACKS];
bool advance_ip; // Should the IP advance after this instruction?
Modified: development/source/cpu/cHardwareBase.cc
===================================================================
--- development/source/cpu/cHardwareBase.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cHardwareBase.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,16 +1,15 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cHardwareBase.cc
+ * Avida
+ *
+ * Created by David on 11/17/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2003 California Institute of Technology.
+ *
+ */
#include "cHardwareBase.h"
-cHardwareBase::~cHardwareBase()
-{
-}
-
bool cHardwareBase::Inst_Nop() // Do Nothing.
{
return true;
Modified: development/source/cpu/cHardwareBase.h
===================================================================
--- development/source/cpu/cHardwareBase.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cHardwareBase.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -40,7 +40,7 @@
{
assert(organism != NULL);
}
- virtual ~cHardwareBase();
+ virtual ~cHardwareBase() { ; }
// -------- Organism ---------
cOrganism* GetOrganism() { return organism; }
Modified: development/source/cpu/cHardwareCPU.cc
===================================================================
--- development/source/cpu/cHardwareCPU.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cHardwareCPU.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1559,21 +1559,21 @@
// Divide Mutations
if (organism->TestDivideMut()) {
- const UINT mut_line = m_world->GetRandom().GetUInt(child_genome.GetSize());
+ const unsigned int mut_line = m_world->GetRandom().GetUInt(child_genome.GetSize());
child_genome[mut_line] = m_inst_set->GetRandomInst();
cpu_stats.mut_stats.divide_mut_count++;
}
// Divide Insertions
if (organism->TestDivideIns() && child_genome.GetSize() < MAX_CREATURE_SIZE){
- const UINT mut_line = m_world->GetRandom().GetUInt(child_genome.GetSize() + 1);
+ const unsigned int mut_line = m_world->GetRandom().GetUInt(child_genome.GetSize() + 1);
child_genome.Insert(mut_line, m_inst_set->GetRandomInst());
cpu_stats.mut_stats.divide_insert_mut_count++;
}
// Divide Deletions
if (organism->TestDivideDel() && child_genome.GetSize() > MIN_CREATURE_SIZE){
- const UINT mut_line = m_world->GetRandom().GetUInt(child_genome.GetSize());
+ const unsigned int mut_line = m_world->GetRandom().GetUInt(child_genome.GetSize());
// if( child_genome.FlagCopied(mut_line) == true) copied_size_change--;
child_genome.Remove(mut_line);
cpu_stats.mut_stats.divide_delete_mut_count++;
@@ -3088,7 +3088,7 @@
bool cHardwareCPU::Inst_SetHead()
{
const int head_used = FindModifiedHead(nHardware::HEAD_IP);
- threads[cur_thread].cur_head = (UCHAR) head_used;
+ threads[cur_thread].cur_head = (unsigned char) head_used;
return true;
}
Modified: development/source/cpu/cHardwareCPU_Thread.cc
===================================================================
--- development/source/cpu/cHardwareCPU_Thread.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cHardwareCPU_Thread.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,20 +1,17 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cHardwareCPU_Thread.cc
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2003 California Institute of Technology.
+ *
+ */
-#ifndef HARDWARE_CPU_THREAD_HH
#include "cHardwareCPU_Thread.h"
-#endif
using namespace std;
-/////////////////////////
-// cHardwareCPU_Thread
-/////////////////////////
-
cHardwareCPU_Thread::cHardwareCPU_Thread(cHardwareBase * in_hardware, int _id)
{
Reset(in_hardware, _id);
Modified: development/source/cpu/cHardwareCPU_Thread.h
===================================================================
--- development/source/cpu/cHardwareCPU_Thread.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cHardwareCPU_Thread.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,16 +1,19 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cHardwareCPU_Thread.h
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2003 California Institute of Technology.
+ *
+ */
-#ifndef HARDWARE_CPU_THREAD_HH
-#define HARDWARE_CPU_THREAD_HH
+#ifndef cHardwareCPU_Thread_h
+#define cHardwareCPU_Thread_h
#include <iostream>
-#ifndef CODE_LABEL_HH
+#ifndef cCodeLabel_h
#include "cCodeLabel.h"
#endif
#ifndef nHardware_h
@@ -19,13 +22,13 @@
#ifndef nHardwareCPU_h
#include "nHardwareCPU.h"
#endif
-#ifndef HEAD_CPU_HH
+#ifndef cHeadCPU_h
#include "cHeadCPU.h"
#endif
-#ifndef CPU_STACK_HH
+#ifndef cCPUStack_h
#include "cCPUStack.h"
#endif
-#ifndef TBUFFER_HH
+#ifndef tBuffer_h
#include "tBuffer.h"
#endif
@@ -48,8 +51,8 @@
int reg[nHardwareCPU::NUM_REGISTERS];
cHeadCPU heads[nHardware::NUM_HEADS];
cCPUStack stack;
- UCHAR cur_stack; // 0 = local stack, 1 = global stack.
- UCHAR cur_head;
+ unsigned char cur_stack; // 0 = local stack, 1 = global stack.
+ unsigned char cur_head;
cCodeLabel read_label;
cCodeLabel next_label;
Modified: development/source/cpu/cHardwareSMT.cc
===================================================================
--- development/source/cpu/cHardwareSMT.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cHardwareSMT.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1157,21 +1157,21 @@
// Divide Mutations
if (organism->TestDivideMut()) {
- const UINT mut_line = m_world->GetRandom().GetUInt(child_genome.GetSize());
+ const unsigned int mut_line = m_world->GetRandom().GetUInt(child_genome.GetSize());
child_genome[mut_line] = m_inst_set->GetRandomInst();
cpu_stats.mut_stats.divide_mut_count++;
}
// Divide Insertions
if (organism->TestDivideIns() && child_genome.GetSize() < MAX_CREATURE_SIZE){
- const UINT mut_line = m_world->GetRandom().GetUInt(child_genome.GetSize() + 1);
+ const unsigned int mut_line = m_world->GetRandom().GetUInt(child_genome.GetSize() + 1);
child_genome.Insert(mut_line, m_inst_set->GetRandomInst());
cpu_stats.mut_stats.divide_insert_mut_count++;
}
// Divide Deletions
if (organism->TestDivideDel() && child_genome.GetSize() > MIN_CREATURE_SIZE){
- const UINT mut_line = m_world->GetRandom().GetUInt(child_genome.GetSize());
+ const unsigned int mut_line = m_world->GetRandom().GetUInt(child_genome.GetSize());
// if( child_genome.FlagCopied(mut_line) == true) copied_size_change--;
child_genome.Remove(mut_line);
cpu_stats.mut_stats.divide_delete_mut_count++;
@@ -1266,19 +1266,19 @@
// Divide Mutations
if (organism->TestDivideMut()) {
- const UINT mut_line = m_world->GetRandom().GetUInt(injected_code.GetSize());
+ const unsigned int mut_line = m_world->GetRandom().GetUInt(injected_code.GetSize());
injected_code[mut_line] = m_inst_set->GetRandomInst();
}
// Divide Insertions
if (organism->TestDivideIns() && injected_code.GetSize() < MAX_CREATURE_SIZE){
- const UINT mut_line = m_world->GetRandom().GetUInt(injected_code.GetSize() + 1);
+ const unsigned int mut_line = m_world->GetRandom().GetUInt(injected_code.GetSize() + 1);
injected_code.Insert(mut_line, m_inst_set->GetRandomInst());
}
// Divide Deletions
if (organism->TestDivideDel() && injected_code.GetSize() > MIN_CREATURE_SIZE){
- const UINT mut_line = m_world->GetRandom().GetUInt(injected_code.GetSize());
+ const unsigned int mut_line = m_world->GetRandom().GetUInt(injected_code.GetSize());
injected_code.Remove(mut_line);
}
Modified: development/source/cpu/cHardwareSMT_Thread.cc
===================================================================
--- development/source/cpu/cHardwareSMT_Thread.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cHardwareSMT_Thread.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -11,10 +11,6 @@
using namespace std;
-/////////////////////////
-// cHardwareSMT_Thread
-/////////////////////////
-
cHardwareSMT_Thread::cHardwareSMT_Thread(cHardwareBase * in_hardware, int _id)
{
Reset(in_hardware, _id);
Modified: development/source/cpu/cHardwareSMT_Thread.h
===================================================================
--- development/source/cpu/cHardwareSMT_Thread.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cHardwareSMT_Thread.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -7,24 +7,24 @@
*
*/
-#ifndef HARDWARE_SMT_THREAD_H
-#define HARDWARE_SMT_THREAD_H
+#ifndef cHardwareSMT_Thread_h
+#define cHardwareSMT_Thread_h
#include <iostream>
-#ifndef CODE_LABEL_HH
+#ifndef cCodeLabel_h
#include "cCodeLabel.h"
#endif
-#ifndef CPU_STACK_HH
+#ifndef cCPUStack_h
#include "cCPUStack.h"
#endif
-#ifndef HEAD_MULTI_MEM_HH
+#ifndef cHeadMultiMem_h
#include "cHeadMultiMem.h"
#endif
-#ifndef HARDWARE_SMT_CONSTANTS_H
+#ifndef nHardwareSMT_h
#include "nHardwareSMT.h"
#endif
-#ifndef TBUFFER_HH
+#ifndef tBuffer_h
#include "tBuffer.h"
#endif
@@ -34,19 +34,15 @@
* @see cCPUStack, cHeadMultiMem, cHardwareSMT
**/
-class cHeadMultiMem; // aggregate
-class cCodeLabel; // aggregate
-class cCPUStack; // aggregate
class cHardwareBase;
class cInjectGenotype;
-template <class T> class tBuffer; // aggregate
struct cHardwareSMT_Thread {
private:
int id;
public:
cHeadMultiMem heads[nHardware::NUM_HEADS];
- UCHAR cur_head;
+ unsigned char cur_head;
cCPUStack local_stacks[nHardwareSMT::NUM_LOCAL_STACKS];
bool advance_ip; // Should the IP advance after this instruction?
Modified: development/source/cpu/cHardwareStatusPrinter.cc
===================================================================
--- development/source/cpu/cHardwareStatusPrinter.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cHardwareStatusPrinter.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,23 +1,25 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2004 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cHardwareStatusPrinter.cc
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2004 California Institute of Technology.
+ *
+ */
+#include "cHardwareStatusPrinter.h"
+
#include "cHeadCPU.h"
#include "cHardware4Stack.h"
#include "cHardwareBase.h"
#include "cHardwareCPU.h"
#include "cHardwareSMT.h"
-#include "cHardwareStatusPrinter.h"
#include "cInstSet.h"
#include "cOrganism.h"
#include "cString.h"
#include "cStringUtil.h"
-#include <fstream>
-
cString cHardwareStatusPrinter::Bonus(const cString &next_name)
{
return cStringUtil::Stringf("%s (bonus instruction)", next_name());
Modified: development/source/cpu/cHardwareStatusPrinter.h
===================================================================
--- development/source/cpu/cHardwareStatusPrinter.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cHardwareStatusPrinter.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,38 +1,37 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2004 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cHardwareStatusPrinter.h
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2004 California Institute of Technology.
+ *
+ */
-#ifndef HARDWARE_STATUS_PRINTER_HH
-#define HARDWARE_STATUS_PRINTER_HH
+#ifndef cHardwareStatusPrinter_h
+#define cHardwareStatusPrinter_h
#include <iostream>
-#ifndef HARDWARE_TRACER_HH
+#ifndef cHardwareTracer_h
#include "cHardwareTracer.h"
#endif
-#ifndef HARDWARE_TRACER_4STACK_HH
+#ifndef cHardwareTracer_4Stack_h
#include "cHardwareTracer_4Stack.h"
#endif
-#ifndef HARDWARE_TRACER_SMT_H
+#ifndef cHardwareTracer_SMT_h
#include "cHardwareTracer_SMT.h"
#endif
-#ifndef HARDWARE_TRACER_CPU_HH
+#ifndef cHardwareTracer_CPU_h
#include "cHardwareTracer_CPU.h"
#endif
-#ifndef HARDWARE_TRACER_TEST_CPU_HH
+#ifndef cHardwareTracer_TestCPU_h
#include "cHardwareTracer_TestCPU.h"
#endif
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
-
-using namespace std;
-
-
class cHardwareBase;
class cHardwareStatusPrinter :
@@ -43,15 +42,15 @@
public cHardwareTracer_TestCPU
{
protected:
- ostream& m_trace_fp;
+ std::ostream& m_trace_fp;
protected:
- const cString & GetNextInstName(cHardwareCPU& hardware);
- const cString & GetNextInstName(cHardware4Stack& hardware);
- const cString & GetNextInstName(cHardwareSMT& hardware);
- cString Bonus(const cString &next_name);
+ const cString& GetNextInstName(cHardwareCPU& hardware);
+ const cString& GetNextInstName(cHardware4Stack& hardware);
+ const cString& GetNextInstName(cHardwareSMT& hardware);
+ cString Bonus(const cString& next_name);
void PrintStatus(cHardwareBase& hardware, const cString& next_name);
public:
- cHardwareStatusPrinter(ostream& trace_fp) : m_trace_fp(trace_fp) {;}
+ cHardwareStatusPrinter(std::ostream& trace_fp) : m_trace_fp(trace_fp) {;}
virtual void TraceHardware_CPU(cHardwareCPU &hardware);
virtual void TraceHardware_4Stack(cHardware4Stack &hardware);
@@ -59,13 +58,8 @@
virtual void TraceHardware_CPUBonus(cHardwareCPU &hardware);
virtual void TraceHardware_4StackBonus(cHardware4Stack &hardware);
virtual void TraceHardware_SMTBonus(cHardwareSMT &hardware);
- virtual void TraceHardware_TestCPU(
- int time_used,
- int time_allocated,
- int size,
- const cString &final_memory,
- const cString &child_memory
- );
+ virtual void TraceHardware_TestCPU(int time_used, int time_allocated, int size,
+ const cString& final_memory, const cString& child_memory);
};
#endif
Modified: development/source/cpu/cHardwareTracer.h
===================================================================
--- development/source/cpu/cHardwareTracer.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cHardwareTracer.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,15 +1,19 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2004 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cHardwareTracer.h
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2004 California Institute of Technology.
+ *
+ */
-#ifndef HARDWARE_TRACER_HH
-#define HARDWARE_TRACER_HH
+#ifndef cHardwareTracer_h
+#define cHardwareTracer_h
-struct cHardwareTracer
+class cHardwareTracer
{
+public:
virtual ~cHardwareTracer() { ; }
};
Modified: development/source/cpu/cHardwareTracer_4Stack.h
===================================================================
--- development/source/cpu/cHardwareTracer_4Stack.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cHardwareTracer_4Stack.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,15 +1,19 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2004 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cHardwareTracer_4Stack.h
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2004 California Institute of Technology.
+ *
+ */
-#ifndef HARDWARE_TRACER_4STACK_HH
-#define HARDWARE_TRACER_4STACK_HH
+#ifndef cHardwareTracer_4Stack_h
+#define cHardwareTracer_4Stack_h
class cHardware4Stack;
-struct cHardwareTracer_4Stack {
+class cHardwareTracer_4Stack {
+public:
virtual ~cHardwareTracer_4Stack() { ; }
virtual void TraceHardware_4Stack(cHardware4Stack &) = 0;
virtual void TraceHardware_4StackBonus(cHardware4Stack &) = 0;
Modified: development/source/cpu/cHardwareTracer_CPU.h
===================================================================
--- development/source/cpu/cHardwareTracer_CPU.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cHardwareTracer_CPU.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,15 +1,20 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2004 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cHardwareTracer_CPU.h
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2004 California Institute of Technology.
+ *
+ */
-#ifndef HARDWARE_TRACER_CPU_HH
-#define HARDWARE_TRACER_CPU_HH
+#ifndef cHardwareTracer_CPU_h
+#define cHardwareTracer_CPU_h
+
class cHardwareCPU;
-struct cHardwareTracer_CPU {
+class cHardwareTracer_CPU {
+public:
virtual ~cHardwareTracer_CPU() { ; }
virtual void TraceHardware_CPU(cHardwareCPU &) = 0;
virtual void TraceHardware_CPUBonus(cHardwareCPU &) = 0;
Modified: development/source/cpu/cHardwareTracer_SMT.h
===================================================================
--- development/source/cpu/cHardwareTracer_SMT.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cHardwareTracer_SMT.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,17 +1,19 @@
/*
- * cHardwareSMT.h
+ * cHardwareTracer_SMT.h
* Avida
*
- * Created by David on 9/22/05.
+ * Created by David on 11/30/05.
* Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2004 California Institute of Technology.
*
*/
-#ifndef HARDWARE_TRACER_SMT_H
-#define HARDWARE_TRACER_SMT_H
+#ifndef cHardwareTracer_SMT_h
+#define cHardwareTracer_SMT_h
class cHardwareSMT;
-struct cHardwareTracer_SMT {
+class cHardwareTracer_SMT {
+public:
virtual ~cHardwareTracer_SMT() { ; }
virtual void TraceHardware_SMT(cHardwareSMT &) = 0;
virtual void TraceHardware_SMTBonus(cHardwareSMT &) = 0;
Modified: development/source/cpu/cHardwareTracer_TestCPU.h
===================================================================
--- development/source/cpu/cHardwareTracer_TestCPU.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cHardwareTracer_TestCPU.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,15 +1,19 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2004 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cHardwareTracer_TestCPU.h
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2004 California Institute of Technology.
+ *
+ */
-#ifndef HARDWARE_TRACER_TEST_CPU_HH
-#define HARDWARE_TRACER_TEST_CPU_HH
+#ifndef cHardwareTracer_TestCPU_h
+#define cHardwareTracer_TestCPU_h
class cString;
-struct cHardwareTracer_TestCPU {
+class cHardwareTracer_TestCPU {
+public:
virtual ~cHardwareTracer_TestCPU() { ; }
virtual void TraceHardware_TestCPU(
int time_used,
Modified: development/source/cpu/cHeadCPU.cc
===================================================================
--- development/source/cpu/cHeadCPU.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cHeadCPU.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,40 +1,24 @@
-/////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cHeadCPU.cc
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2003 California Institute of Technology.
+ *
+ */
-#ifndef HEAD_CPU_HH
#include "cHeadCPU.h"
-#endif
-#ifndef CPU_MEMORY_HH
#include "cCPUMemory.h"
-#endif
-#ifndef CODE_LABEL_HH
#include "cCodeLabel.h"
-#endif
-#ifndef GENOME_HH
#include "cGenome.h"
-#endif
-#ifndef HARDWARE_BASE_HH
#include "cHardwareBase.h"
-#endif
-#ifndef cInstSet_h
#include "cInstSet.h"
-#endif
-#ifndef INSTRUCTION_HH
#include "cInstruction.h"
-#endif
#include <assert.h>
-class cHardwareBase; // access
-class cCPUMemory; // access
-class cCodeLabel; // access
-class cInstSet; // access
-
cHeadCPU::cHeadCPU() {
main_hardware = NULL;
cur_hardware = NULL;
@@ -44,7 +28,7 @@
cHeadCPU::cHeadCPU(cHardwareBase * in_hardware, int in_pos) {
main_hardware = in_hardware;
cur_hardware = in_hardware;
-
+
position = in_pos;
if (in_pos) Adjust();
}
@@ -61,12 +45,12 @@
{
assert(cur_hardware != NULL);
assert(main_hardware != NULL);
-
+
const int mem_size = cur_hardware->GetMemory().GetSize();
-
+
// If we are still in range, stop here!
if (position >= 0 && position < mem_size) return;
-
+
// If the memory is gone, just stick it at the begining of its parent.
if (mem_size == 0) {
cur_hardware = main_hardware;
@@ -82,7 +66,7 @@
position %= GetMemory().GetSize();
}
}
-
+
}
@@ -101,27 +85,27 @@
if (label.GetSize() == 0) {
return *this;
}
-
+
int found_pos = -1;
-
+
// Call special functions depending on if jump is forwards or backwards.
if( direction < 0 ) {
found_pos =
- FindLabel_Backward(label, GetMemory(), GetPosition() - label.GetSize());
+ FindLabel_Backward(label, GetMemory(), GetPosition() - label.GetSize());
}
-
+
// Jump forwards.
else {
found_pos = FindLabel_Forward(label, GetMemory(), GetPosition());
}
-
+
if (found_pos >= 0) {
// Return the last line of the found label, or the starting point.
cHeadCPU search_head(*this);
search_head.Set(found_pos - 1);
return search_head;
}
-
+
// It wasn't found; return the starting position of the instruction pointer.
return *this;
}
@@ -149,7 +133,7 @@
void cHeadCPU::LoopJump(int jump)
{
position += jump;
-
+
// If we are out of range, bring back in.
if (position < 0 || position >= GetMemory().GetSize()) {
position %= GetMemory().GetSize();
@@ -191,7 +175,7 @@
const cInstruction & cHeadCPU::GetInst(int offset) const {
int new_pos = position + offset;
-
+
return GetMemory()[new_pos];
}
@@ -306,85 +290,85 @@
return operator--();
}
-
+
// Search forwards for search_label from _after_ position pos in the
// memory. Return the first line _after_ the the found label. It is okay
// to find search label's match inside another label.
int cHeadCPU::FindLabel_Forward(const cCodeLabel & search_label,
- const cGenome & search_mem, int pos)
+ const cGenome & search_mem, int pos)
{
assert (pos < search_mem.GetSize() && pos >= 0);
-
+
int search_start = pos;
int label_size = search_label.GetSize();
bool found_label = false;
const cInstSet & inst_set = main_hardware->GetInstSet();
-
+
// Move off the template we are on.
pos += label_size;
// Search until we find the complement or exit the memory.
while (pos < search_mem.GetSize()) {
-
+
// If we are within a label, rewind to the beginning of it and see if
// it has the proper sub-label that we're looking for.
-
+
if (inst_set.IsNop(search_mem[pos])) {
// Find the start and end of the label we're in the middle of.
-
+
int start_pos = pos;
int end_pos = pos + 1;
while (start_pos > search_start &&
- inst_set.IsNop( search_mem[start_pos - 1] )) {
- start_pos--;
+ inst_set.IsNop( search_mem[start_pos - 1] )) {
+ start_pos--;
}
while (end_pos < search_mem.GetSize() &&
- inst_set.IsNop( search_mem[end_pos] )) {
- end_pos++;
+ inst_set.IsNop( search_mem[end_pos] )) {
+ end_pos++;
}
int test_size = end_pos - start_pos;
-
+
// See if this label has the proper sub-label within it.
int max_offset = test_size - label_size + 1;
for (int offset = start_pos; offset < start_pos + max_offset; offset++) {
-
- // Test the number of matches for this offset.
- int matches;
- for (matches = 0; matches < label_size; matches++) {
- if (search_label[matches] !=
- inst_set.GetNopMod( search_mem[offset + matches] )) {
- break;
- }
- }
-
- // If we have found it, break out of this loop!
- if (matches == label_size) {
- found_label = true;
- break;
- }
+
+ // Test the number of matches for this offset.
+ int matches;
+ for (matches = 0; matches < label_size; matches++) {
+ if (search_label[matches] !=
+ inst_set.GetNopMod( search_mem[offset + matches] )) {
+ break;
+ }
+ }
+
+ // If we have found it, break out of this loop!
+ if (matches == label_size) {
+ found_label = true;
+ break;
+ }
}
-
+
// If we've found the complement label, set the position to the end of
// the label we found it in, and break out.
-
+
if (found_label == true) {
- pos = end_pos;
- break;
+ pos = end_pos;
+ break;
}
-
+
// We haven't found it; jump pos to just after the current label being
// checked.
pos = end_pos;
}
-
+
// Jump up a block to the next possible point to find a label,
pos += label_size;
}
-
+
// If the label was not found return a -1.
if (found_label == false) pos = -1;
-
+
return pos;
}
@@ -393,15 +377,15 @@
// to find search label's match inside another label.
int cHeadCPU::FindLabel_Backward(const cCodeLabel & search_label,
- const cGenome & search_mem, int pos)
+ const cGenome & search_mem, int pos)
{
assert (pos < search_mem.GetSize());
-
+
int search_start = pos;
int label_size = search_label.GetSize();
bool found_label = false;
const cInstSet & inst_set = main_hardware->GetInstSet();
-
+
// Move off the template we are on.
pos -= label_size;
@@ -409,67 +393,67 @@
while (pos >= 0) {
// If we are within a label, rewind to the beginning of it and see if
// it has the proper sub-label that we're looking for.
-
+
if (inst_set.IsNop( search_mem[pos] )) {
// Find the start and end of the label we're in the middle of.
-
+
int start_pos = pos;
int end_pos = pos + 1;
while (start_pos > 0 && inst_set.IsNop(search_mem[start_pos - 1])) {
- start_pos--;
+ start_pos--;
}
while (end_pos < search_start &&
- inst_set.IsNop( search_mem[end_pos] )) {
- end_pos++;
+ inst_set.IsNop( search_mem[end_pos] )) {
+ end_pos++;
}
int test_size = end_pos - start_pos;
-
+
// See if this label has the proper sub-label within it.
int max_offset = test_size - label_size + 1;
for (int offset = start_pos; offset < start_pos + max_offset; offset++) {
-
- // Test the number of matches for this offset.
- int matches;
- for (matches = 0; matches < label_size; matches++) {
- if (search_label[matches] !=
- inst_set.GetNopMod( search_mem[offset + matches] )) {
- break;
- }
- }
-
- // If we have found it, break out of this loop!
- if (matches == label_size) {
- found_label = true;
- break;
- }
+
+ // Test the number of matches for this offset.
+ int matches;
+ for (matches = 0; matches < label_size; matches++) {
+ if (search_label[matches] !=
+ inst_set.GetNopMod( search_mem[offset + matches] )) {
+ break;
+ }
+ }
+
+ // If we have found it, break out of this loop!
+ if (matches == label_size) {
+ found_label = true;
+ break;
+ }
}
-
+
// If we've found the complement label, set the position to the end of
// the label we found it in, and break out.
-
+
if (found_label == true) {
- pos = end_pos;
- break;
+ pos = end_pos;
+ break;
}
-
+
// We haven't found it; jump pos to just before the current label
// being checked.
pos = start_pos - 1;
}
-
+
// Jump up a block to the next possible point to find a label,
pos -= label_size;
}
-
+
// If the label was not found return a -1.
if (found_label == false) pos = -1;
-
+
return pos;
}
bool cHeadCPU::operator==(const cHeadCPU & in_cpu_head) const {
return (cur_hardware == in_cpu_head.cur_hardware) &&
- (position == in_cpu_head.position);
+ (position == in_cpu_head.position);
}
bool cHeadCPU::AtEnd() const
Modified: development/source/cpu/cHeadCPU.h
===================================================================
--- development/source/cpu/cHeadCPU.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cHeadCPU.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,28 +1,27 @@
-/////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cHeadCPU.h
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2003 California Institute of Technology.
+ *
+ */
-#ifndef HEAD_CPU_HH
-#define HEAD_CPU_HH
+#ifndef cHeadCPU_h
+#define cHeadCPU_h
-#ifndef DEFS_HH
+#ifndef defs_h
#include "defs.h"
#endif
-class cHardwareBase;
-class cCodeLabel;
-class cGenome;
-class cCPUMemory;
-
/**
* The cHeadCPU class contains a pointer to locations in memory for a CPU.
**/
class cHardwareBase;
class cCodeLabel;
+class cCPUMemory;
class cGenome;
class cInstruction;
Modified: development/source/cpu/cHeadMultiMem.cc
===================================================================
--- development/source/cpu/cHeadMultiMem.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cHeadMultiMem.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,39 +1,22 @@
-/////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cHeadMultiMem.cc
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2003 California Institute of Technology.
+ *
+ */
-#ifndef HEAD_MULTI_MEM_HH
#include "cHeadMultiMem.h"
-#endif
-#ifndef CPU_MEMORY_HH
#include "cCPUMemory.h"
-#endif
-#ifndef HARDWARE_BASE_HH
#include "cHardwareBase.h"
-#endif
-#ifndef cInstSet_h
#include "cInstSet.h"
-#endif
-#ifndef INSTRUCTION_HH
#include "cInstruction.h"
-#endif
#include <assert.h>
-cHeadMultiMem::cHeadMultiMem() : cHeadCPU() { mem_space=0; }
-
-cHeadMultiMem::cHeadMultiMem(cHardwareBase * in_hardware, int in_pos, int in_mem_space)
- : cHeadCPU(in_hardware, in_pos) { mem_space = in_mem_space; }
-
-cHeadMultiMem::cHeadMultiMem(const cHeadMultiMem & in_head) : cHeadCPU(in_head)
-{
- mem_space = in_head.mem_space;
-}
-
void cHeadMultiMem::Adjust()
{
assert(cur_hardware != NULL);
Modified: development/source/cpu/cHeadMultiMem.h
===================================================================
--- development/source/cpu/cHeadMultiMem.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cHeadMultiMem.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,34 +1,28 @@
-/////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cHeadMultiMem.h
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2003 California Institute of Technology.
+ *
+ */
-#ifndef HEAD_MULTI_MEM_HH
-#define HEAD_MULTI_MEM_HH
+#ifndef cHeadMultiMem_h
+#define cHeadMultiMem_h
-#ifndef HEAD_CPU_HH
+#ifndef cHeadCPU_h
#include "cHeadCPU.h"
#endif
-#ifndef DEFS_HH
-#include "defs.h"
-#endif
-class cCodeLabel;
-class cCPUMemory;
-class cGenome;
-class cHardwareBase;
-class cInstruction;
-
class cHeadMultiMem : public cHeadCPU {
private:
int mem_space;
public:
- cHeadMultiMem();
- cHeadMultiMem(cHardwareBase* in_hardware, int in_pos = 0, int mem_space = 0);
- cHeadMultiMem(const cHeadMultiMem& in_cpu_head);
+ cHeadMultiMem() : cHeadCPU() { mem_space = 0; }
+ cHeadMultiMem(cHardwareBase* hw, int pos = 0, int ms = 0) : cHeadCPU(hw, pos) { mem_space = ms; }
+ cHeadMultiMem(const cHeadMultiMem& in_head) : cHeadCPU(in_head) { mem_space = in_head.mem_space; }
void Adjust();
void Reset(int in_mem_space = 0, cHardwareBase* new_hardware = NULL);
Modified: development/source/cpu/cInstLibCPU.h
===================================================================
--- development/source/cpu/cInstLibCPU.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cInstLibCPU.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,23 +1,27 @@
-#ifndef INST_LIB_CPU_HH
-#define INST_LIB_CPU_HH
+/*
+ * cInstLibCPU.h
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ *
+ */
+#ifndef cInstLibCPU_h
+#define cInstLibCPU_h
-#ifndef INST_LIB_BASE_HH
+#ifndef cInstLibBase_h
#include "cInstLibBase.h"
#endif
-
#ifndef cHardwareCPU_h
#include "cHardwareCPU.h"
#endif
-#ifndef INSTRUCTION_HH
+#ifndef cInstruction_h
#include "cInstruction.h"
#endif
-///////////////
-// cInstLibCPU
-///////////////
+class cString;
-class cString;
class cInstLibCPU : public cInstLibBase {
const size_t m_nopmods_array_size;
const size_t m_function_array_size;
Modified: development/source/cpu/cMemoryFlags.h
===================================================================
--- development/source/cpu/cMemoryFlags.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cMemoryFlags.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,12 +1,15 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cMemoryFlags.h
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2003 California Institute of Technology.
+ *
+ */
-#ifndef MEMORY_FLAGS_HH
-#define MEMORY_FLAGS_HH
+#ifndef cMemoryFlags_h
+#define cMemoryFlags_h
class cMemoryFlags {
friend class cCPUMemory;
Modified: development/source/cpu/cTestCPU.cc
===================================================================
--- development/source/cpu/cTestCPU.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cTestCPU.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cTestCPU.cc
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2003 California Institute of Technology.
+ *
+ */
#include "cTestCPU.h"
@@ -282,17 +285,17 @@
#ifdef QUICK_BASE_TEST_CPU
// This checks to make sure a 'copy', 'divide', and 'allocate' are all in
// the creatures, and if not doesn't even bother to test it.
- static UCHAR copy_id = inst_set->GetInstID("copy");
- static UCHAR div_id = inst_set->GetInstID("divide");
- static UCHAR alloc_id = inst_set->GetInstID("allocate");
+ static unsigned char copy_id = inst_set->GetInstID("copy");
+ static unsigned char div_id = inst_set->GetInstID("divide");
+ static unsigned char alloc_id = inst_set->GetInstID("allocate");
#endif
#ifdef QUICK_HEAD_TEST_CPU
// This checks to make sure a 'copy', 'divide', and 'allocate' are all in
// the creatures, and if not doesn't even bother to test it.
- static UCHAR copy_id = inst_set->GetInstID("h-copy");
- static UCHAR div_id = inst_set->GetInstID("h-divide");
- static UCHAR alloc_id = inst_set->GetInstID("h-alloc");
+ static unsigned char copy_id = inst_set->GetInstID("h-copy");
+ static unsigned char div_id = inst_set->GetInstID("h-divide");
+ static unsigned char alloc_id = inst_set->GetInstID("h-alloc");
#endif
Modified: development/source/cpu/cTestCPU.h
===================================================================
--- development/source/cpu/cTestCPU.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cTestCPU.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cTestCPU.h
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2003 California Institute of Technology.
+ *
+ */
#ifndef cTestCPU_h
#define cTestCPU_h
Modified: development/source/cpu/cTestUtil.cc
===================================================================
--- development/source/cpu/cTestUtil.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cTestUtil.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2001 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cTestUtil.cc
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2003 California Institute of Technology.
+ *
+ */
#include "cTestUtil.h"
@@ -25,7 +28,6 @@
#include <fstream>
#include <iomanip>
-
using namespace std;
Modified: development/source/cpu/cTestUtil.h
===================================================================
--- development/source/cpu/cTestUtil.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/cTestUtil.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,14 +1,17 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cTestUtil.h
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2003 California Institute of Technology.
+ *
+ */
-#ifndef TEST_UTIL_HH
-#define TEST_UTIL_HH
+#ifndef cTestUtil_h
+#define cTestUtil_h
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
@@ -25,9 +28,9 @@
class cTestUtil {
public:
static void PrintGenome(cWorld* world, const cGenome & genome, cString filename="",
- cGenotype * genotype=NULL, int update_out=-1);
+ cGenotype * genotype=NULL, int update_out=-1);
static void PrintGenome(cWorld* world, cInjectGenotype * genotype, const cGenome & genome,
- cString filename="", int update_out=-1);
+ cString filename="", int update_out=-1);
};
#endif
Modified: development/source/cpu/nHardware4Stack.h
===================================================================
--- development/source/cpu/nHardware4Stack.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/nHardware4Stack.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,16 +1,18 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * nHardware4Stack.h
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2003 California Institute of Technology.
+ *
+ */
-#ifndef HARDWARE_4STACK_CONSTANTS_HH
-#define HARDWARE_4STACK_CONSTANTS_HH
+#ifndef nHardware4Stack_h
+#define nHardware4Stack_h
namespace nHardware4Stack
{
- //new-style constant declarations - law
static const int NUM_LOCAL_STACKS = 5;
static const int NUM_GLOBAL_STACKS = 1;
static const int NUM_STACKS = NUM_LOCAL_STACKS + NUM_GLOBAL_STACKS;
Modified: development/source/cpu/nHardwareCPU.h
===================================================================
--- development/source/cpu/nHardwareCPU.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/nHardwareCPU.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,11 +1,13 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * nHardwareCPU.h
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2003 California Institute of Technology.
+ *
+ */
-
#ifndef nHardwareCPU_h
#define nHardwareCPU_h
Modified: development/source/cpu/nHardwareSMT.h
===================================================================
--- development/source/cpu/nHardwareSMT.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/nHardwareSMT.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -7,10 +7,9 @@
*
*/
-#ifndef HARDWARE_SMT_CONSTANTS_H
-#define HARDWARE_SMT_CONSTANTS_H
+#ifndef nHardwareSMT_h
+#define nHardwareSMT_h
-// Constants can be used across different cpu models, wrap in namespace @DMB
namespace nHardwareSMT
{
static const int NUM_LOCAL_STACKS = 3;
Modified: development/source/cpu/sCPUStats.h
===================================================================
--- development/source/cpu/sCPUStats.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/sCPUStats.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * sCPUStats.h
+ * Avida
+ *
+ * Created by David on 11/30/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1999-2003 California Institute of Technology.
+ *
+ */
#ifndef sCPUStats_h
#define sCPUStats_h
Modified: development/source/cpu/tInstLib.h
===================================================================
--- development/source/cpu/tInstLib.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/cpu/tInstLib.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -7,13 +7,13 @@
*
*/
-#ifndef TINSTLIB_H
-#define TINSTLIB_H
+#ifndef tInstLib_h
+#define tInstLib_h
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
-#ifndef INST_LIB_BASE_HH
+#ifndef cInstLibBase_h
#include "cInstLibBase.h"
#endif
Modified: development/source/defs.h
===================================================================
--- development/source/defs.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/defs.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,25 +1,19 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * defs.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef DEFS_HH
-#define DEFS_HH
+#ifndef defs_h
+#define defs_h
#define VERSION "2.5.0"
#define VERSION_TAG "Jedi"
-/*
-FIXME: remove asap, switching to file-configureable option
-*/
-// path to html doc files
-#ifndef HTMLDIR
-#define HTMLDIR "../work/doc_html/"
-#endif
-
-
// -= Various view modes =-
#define VIEW_NEWVIEWER
// #define VIEW_VISTA
@@ -108,10 +102,6 @@
#undef UNIT
#endif
- #ifdef UCHAR
- #undef UCHAR
- #endif
-
#include <windows.h> // Defines, prototypes, etc. for
#endif
@@ -137,12 +127,6 @@
#define NULL 0
#endif
-#ifndef _WINDEF_ // Defined by WINDOWS.H
- #define UCHAR unsigned char
- #undef UINT
- #define UINT unsigned int
-#endif
-
#define TOOLS_DIR tools
#define CPU_DIR cpu
#define MAIN_DIR main
Modified: development/source/event/CMakeLists.txt
===================================================================
--- development/source/event/CMakeLists.txt 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/event/CMakeLists.txt 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,7 +1,6 @@
SET(libevent_a_SOURCES
cEventManager.cc
cEventList.cc
- cEventListIterator.cc
cEventTriggers.cc
)
Modified: development/source/event/cEvent.h
===================================================================
--- development/source/event/cEvent.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/event/cEvent.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,14 +1,17 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cEvent.h
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef EVENT_HH
-#define EVENT_HH
+#ifndef cEvent_h
+#define cEvent_h
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
Modified: development/source/event/cEventList.cc
===================================================================
--- development/source/event/cEventList.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/event/cEventList.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cEventList.cc
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
#include "cEventList.h"
@@ -18,11 +21,7 @@
using namespace std;
-class cEvent;
-/////////////////
-// cEventList
-/////////////////
cEventList::cEventList( cEventManager* factory_manager, cEventTriggers *triggers ) :
m_factory_manager( factory_manager ),
m_triggers( triggers ),
Modified: development/source/event/cEventList.h
===================================================================
--- development/source/event/cEventList.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/event/cEventList.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,27 +1,23 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cEventList.h
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-/* cEventList.h *************************************************************
- Builds a queue for holding and processing events
+#ifndef cEventList_h
+#define cEventList_h
- charles at krl.caltech.edu & travc at ugcs.caltech.edu
-
-******************************************************************************/
-
-#ifndef EVENT_LIST_HH
-#define EVENT_LIST_HH
-
-#ifndef EVENT_LIST_ENTRY_HH
+#ifndef cEventListEntry_h
#include "cEventListEntry.h"
#endif
-#ifndef EVENT_LIST_ITERATOR_HH
+#ifndef cEventListIterator_h
#include "cEventListIterator.h"
#endif
-#ifndef EVENT_TRIGGERS_HH
+#ifndef cEventTriggers_h
#include "cEventTriggers.h"
#endif
@@ -33,9 +29,6 @@
class cEvent;
class cEventManager;
-class cEventListEntry; // access
-class cEventListIterator; // access
-class cEventTriggers; // access
class cString;
class cEventList {
Modified: development/source/event/cEventListEntry.h
===================================================================
--- development/source/event/cEventListEntry.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/event/cEventListEntry.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,19 +1,22 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cEventListEntry.h
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef EVENT_LIST_ENTRY_HH
-#define EVENT_LIST_ENTRY_HH
+#ifndef cEventListEntry_h
+#define cEventListEntry_h
#include <assert.h>
-#ifndef EVENT_HH
+#ifndef cEvent_h
#include "cEvent.h"
#endif
-#ifndef EVENT_TRIGGERS_HH
+#ifndef cEventTriggers_h
#include "cEventTriggers.h"
#endif
@@ -22,9 +25,6 @@
* @ref cEventList. There is no need to use it in any other context.
**/
-class cEvent; // access
-class cEventTriggers; // access
-
class cEventListEntry {
private:
cEvent *m_event;
Deleted: development/source/event/cEventListIterator.cc
===================================================================
--- development/source/event/cEventListIterator.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/event/cEventListIterator.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,27 +0,0 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
-
-#ifndef EVENT_LIST_ITERATOR_HH
-#include "cEventListIterator.h"
-#endif
-
-#ifndef EVENT_LIST_HH
-#include "cEventList.h"
-#endif
-
-using namespace std;
-
-/////////////////
-// cEventListIterator
-// added by kaben.
-/////////////////
-
-void
-cEventListIterator::PrintEvent(ostream& os){
- cEventList::PrintEvent(m_node, os);
-}
-
Modified: development/source/event/cEventListIterator.h
===================================================================
--- development/source/event/cEventListIterator.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/event/cEventListIterator.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,16 +1,19 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cEventListIterator.h
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef EVENT_LIST_ITERATOR_HH
-#define EVENT_LIST_ITERATOR_HH
+#ifndef cEventListIterator_h
+#define cEventListIterator_h
#include <iostream>
-#ifndef EVENT_LIST_ENTRY_HH
+#ifndef cEventListEntry_h
#include "cEventListEntry.h"
#endif
@@ -21,8 +24,6 @@
* added by Kaben.
**/
-class cEventListEntry; // access
-
class cEventListIterator {
private:
cEventListEntry *m_node;
@@ -31,8 +32,6 @@
cEventListIterator(cEventListEntry *node) : m_node(node) {}
cEventListIterator(const cEventListIterator &it) : m_node(it.m_node) {}
- void PrintEvent(std::ostream& os = std::cout);
-
bool operator==(const cEventListIterator &it) const {
return m_node == it.m_node;
}
Modified: development/source/event/cEventManager.cc
===================================================================
--- development/source/event/cEventManager.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/event/cEventManager.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,3 +1,12 @@
+/*
+ * cEventManager.cc
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
#include "cEventManager.h"
Modified: development/source/event/cEventManager.h
===================================================================
--- development/source/event/cEventManager.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/event/cEventManager.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,20 +1,23 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cEventManager.h
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
#ifndef cEventManager_h
#define cEventManager_h
-#ifndef TLIST_HH
+#ifndef tList_h
#include "tList.h"
#endif
-#ifndef TOBJECTFACTORY_H
+#ifndef tObjectFactory_h
#include "tObjectFactory.h"
#endif
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
Modified: development/source/event/cEventTriggers.cc
===================================================================
--- development/source/event/cEventTriggers.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/event/cEventTriggers.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,22 +1,20 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cEventTriggers.cc
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef EVENT_TRIGGERS_HH
#include "cEventTriggers.h"
-#endif
#include <float.h> // for DBL_MIN
#include <iostream>
using namespace std;
-/////////////////
-// cEventTriggers
-/////////////////
double const cEventTriggers::TRIGGER_BEGIN = DBL_MIN;
double const cEventTriggers::TRIGGER_END = DBL_MAX;
Modified: development/source/event/cEventTriggers.h
===================================================================
--- development/source/event/cEventTriggers.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/event/cEventTriggers.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,12 +1,15 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cEventTriggers.h
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef EVENT_TRIGGERS_HH
-#define EVENT_TRIGGERS_HH
+#ifndef cEventTriggers_h
+#define cEventTriggers_h
/**
* This class is used to physically separate the whole event list business
Modified: development/source/main/CMakeLists.txt
===================================================================
--- development/source/main/CMakeLists.txt 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/CMakeLists.txt 2005-12-07 23:44:39 UTC (rev 414)
@@ -18,7 +18,6 @@
cLocalMutations.cc
cMutationLib.cc
cMutationRates.cc
- cMutation.cc
cMxCodeArray.cc
cOrgMessage.cc
cOrganism.cc
@@ -28,8 +27,6 @@
cPopulationInterface.cc
cReaction.cc
cReactionLib.cc
- cReactionProcess.cc
- cReactionRequisite.cc
cReactionResult.cc
cResource.cc
cResourceCount.cc
@@ -37,7 +34,6 @@
cSpatialCountElem.cc
cSpatialResCount.cc
cStats.cc
- cTaskEntry.cc
cTaskLib.cc
cWorld.cc
)
Modified: development/source/main/MyCodeArrayLessThan.h
===================================================================
--- development/source/main/MyCodeArrayLessThan.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/MyCodeArrayLessThan.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,14 +1,17 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * MyCodeArrayLessThan.h
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef MY_CODE_ARRAY_LESS_THAN_HH
-#define MY_CODE_ARRAY_LESS_THAN_HH
+#ifndef MyCodeArrayLessThan_h
+#define MyCodeArrayLessThan_h
-#ifndef MX_CODE_ARRAY_HH
+#ifndef cMxCodeArray_h
#include "cMxCodeArray.h"
#endif
Modified: development/source/main/avida.cc
===================================================================
--- development/source/main/avida.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/avida.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * avida.cc
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
#include "avida.h"
Modified: development/source/main/avida.h
===================================================================
--- development/source/main/avida.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/avida.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2001 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * avida.h
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2001 California Institute of Technology.
+ *
+ */
#ifndef avida_h
#define avida_h
Modified: development/source/main/cAvidaConfig.cc
===================================================================
--- development/source/main/cAvidaConfig.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cAvidaConfig.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -3,6 +3,7 @@
* Avida
*
* Created by David on 10/16/05.
+ * Designed by Charles.
* Copyright 2005 Michigan State University. All rights reserved.
*
*/
Modified: development/source/main/cAvidaDriver_Analyze.cc
===================================================================
--- development/source/main/cAvidaDriver_Analyze.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cAvidaDriver_Analyze.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,35 +1,27 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cAvidaDriver_Analyze.cc
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
#include "cAvidaDriver_Analyze.h"
#include "cAnalyze.h"
-#include "cWorld.h"
#include <iostream>
using namespace std;
-//////////////////////////
-// cAvidaDriver_Analyze
-//////////////////////////
-cAvidaDriver_Analyze::cAvidaDriver_Analyze(cWorld* world, bool _interactive)
-: interactive(_interactive), m_world(world)
-{
-}
-
-cAvidaDriver_Analyze::~cAvidaDriver_Analyze() { delete m_world; }
-
void cAvidaDriver_Analyze::Run()
{
cout << "In analyze mode!!" << endl;
cAnalyze analyze(m_world);
- if (interactive == true) {
+ if (m_interactive == true) {
analyze.RunInteractive();
}
}
Modified: development/source/main/cAvidaDriver_Analyze.h
===================================================================
--- development/source/main/cAvidaDriver_Analyze.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cAvidaDriver_Analyze.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,16 +1,19 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cAvidaDriver_Analyze.h
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef AVIDA_DRIVER_ANALYZE_HH
-#define AVIDA_DRIVER_ANALYZE_HH
+#ifndef cAvidaDriver_Analyze_h
+#define cAvidaDriver_Analyze_h
#include <cstdlib>
-#ifndef AVIDA_DRIVER_BASE_HH
+#ifndef cAvidaDriver_Base_h
#include "cAvidaDriver_Base.h"
#endif
@@ -18,11 +21,11 @@
class cAvidaDriver_Analyze : public cAvidaDriver_Base {
protected:
- bool interactive;
+ bool m_interactive;
cWorld* m_world;
public:
- cAvidaDriver_Analyze(cWorld* world, bool _interactive=false);
- ~cAvidaDriver_Analyze();
+ cAvidaDriver_Analyze(cWorld* world, bool inter = false) : m_interactive(inter), m_world(world) { ; }
+ ~cAvidaDriver_Analyze() { delete m_world; }
virtual void Run();
};
Modified: development/source/main/cAvidaDriver_Base.cc
===================================================================
--- development/source/main/cAvidaDriver_Base.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cAvidaDriver_Base.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,17 +1,16 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cAvidaDriver_Base.cc
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef AVIDA_DRIVER_BASE_HH
#include "cAvidaDriver_Base.h"
-#endif
-#ifndef STRING_HH
#include "cString.h"
-#endif
#include <iostream>
@@ -21,12 +20,8 @@
// Static variable definitions
cAvidaDriver_Base * cAvidaDriver_Base::main_driver = NULL;
-///////////////////////
-// cAvidaDriver_Base
-///////////////////////
-cAvidaDriver_Base::cAvidaDriver_Base()
- : done_flag(false)
+cAvidaDriver_Base::cAvidaDriver_Base() : done_flag(false)
{
}
Modified: development/source/main/cAvidaDriver_Base.h
===================================================================
--- development/source/main/cAvidaDriver_Base.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cAvidaDriver_Base.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,12 +1,15 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cAvidaDriver_Base.h
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef AVIDA_DRIVER_BASE_HH
-#define AVIDA_DRIVER_BASE_HH
+#ifndef cAvidaDriver_Base_h
+#define cAvidaDriver_Base_h
/**
* cAvidaDriver_Base
@@ -17,6 +20,7 @@
**/
class cString;
+
class cAvidaDriver_Base {
protected:
bool done_flag; // This is set to true when run should finish.
Modified: development/source/main/cAvidaDriver_Population.cc
===================================================================
--- development/source/main/cAvidaDriver_Population.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cAvidaDriver_Population.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cAvidaDriver_Popultion.cc
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
#include "cAvidaDriver_Population.h"
@@ -22,9 +25,6 @@
using namespace std;
-/////////////////////////////
-// cAvidaDriver_Population
-/////////////////////////////
void cAvidaDriver_Population::Run()
{
Modified: development/source/main/cAvidaDriver_Population.h
===================================================================
--- development/source/main/cAvidaDriver_Population.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cAvidaDriver_Population.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,17 +1,20 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cAvidaDriver_Population.h
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef AVIDA_DRIVER_POPULATION_HH
-#define AVIDA_DRIVER_POPULATION_HH
+#ifndef cAvidaDriver_Population_h
+#define cAvidaDriver_Population_h
-#ifndef AVIDA_DRIVER_BASE_HH
+#ifndef cAvidaDriver_Base_h
#include "cAvidaDriver_Base.h"
#endif
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
#ifndef cWorld_h
Modified: development/source/main/cAvidaTriggers.h
===================================================================
--- development/source/main/cAvidaTriggers.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cAvidaTriggers.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,17 +1,20 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cAvidaTriggers.h
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef AVIDA_TRIGGERS_HH
-#define AVIDA_TRIGGERS_HH
+#ifndef cAvidaTriggers_h
+#define cAvidaTriggers_h
-#ifndef EVENT_TRIGGERS_HH
+#ifndef cEventTriggers_h
#include "cEventTriggers.h"
#endif
-#ifndef STATS_HH
+#ifndef cStats_h
#include "cStats.h"
#endif
Modified: development/source/main/cBirthChamber.cc
===================================================================
--- development/source/main/cBirthChamber.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cBirthChamber.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2004 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cBirthChamber.cc
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
#include "cBirthChamber.h"
Modified: development/source/main/cBirthChamber.h
===================================================================
--- development/source/main/cBirthChamber.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cBirthChamber.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,17 +1,20 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cBirthChamber.h
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef BIRTH_CHAMBER_HH
-#define BIRTH_CHAMBER_HH
+#ifndef cBirthChamber_h
+#define cBirthChamber_h
-#ifndef CPU_MEMORY_HH
+#ifndef cCPUMemory_h
#include "cCPUMemory.h"
#endif
-#ifndef MERIT_HH
+#ifndef cMerit_h
#include "cMerit.h"
#endif
Modified: development/source/main/cEnvironment.cc
===================================================================
--- development/source/main/cEnvironment.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cEnvironment.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cEnvironment.cc
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
#include "cEnvironment.h"
@@ -24,6 +27,7 @@
using namespace std;
+
bool cEnvironment::ParseSetting(cString entry, cString & var_name,
cString & var_value, const cString & var_type)
{
Modified: development/source/main/cEnvironment.h
===================================================================
--- development/source/main/cEnvironment.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cEnvironment.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,47 +1,42 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cEnvironment.h
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef ENVIRONMENT_HH
-#define ENVIRONMENT_HH
+#ifndef cEnvironment_h
+#define cEnvironment_h
#ifndef cInstSet_h
#include "cInstSet.h"
#endif
-#ifndef MUTATION_LIB_HH
+#ifndef cMutationLib_h
#include "cMutationLib.h"
#endif
-#ifndef MUTATION_RATES_HH
+#ifndef cMutationRates_h
#include "cMutationRates.h"
#endif
-#ifndef REACTION_LIB_HH
+#ifndef cReactionLib_h
#include "cReactionLib.h"
#endif
-#ifndef RESOURCE_LIB_HH
+#ifndef cResourceLib_h
#include "cResourceLib.h"
#endif
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
-#ifndef TASK_LIB_HH
+#ifndef cTaskLib_h
#include "cTaskLib.h"
#endif
-#ifndef TLIST_HH
+#ifndef tList_h
#include "tList.h"
#endif
-class cResourceLib; // aggregate
-class cReactionLib; // aggregate
-class cMutationLib; // aggregate
-class cTaskLib; // aggregate
-class cInstSet; // aggregate
-class cMutationRates; // aggregate
-class cString; // aggregate
class cReaction;
-template <class T> class tList;
class cReactionRequisite;
template <class T> class tArray;
class cReactionProcess;
Modified: development/source/main/cFitnessMatrix.cc
===================================================================
--- development/source/main/cFitnessMatrix.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cFitnessMatrix.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,17 +1,16 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cFitnessMatrix.cc
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef FITNESS_MATRIX_HH
#include "cFitnessMatrix.h"
-#endif
-#ifndef cInstSet_h
#include "cInstSet.h"
-#endif
using namespace std;
Modified: development/source/main/cFitnessMatrix.h
===================================================================
--- development/source/main/cFitnessMatrix.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cFitnessMatrix.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,12 +1,15 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cFitnessMatrix.h
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef FITNESS_MATRIX_HH
-#define FITNESS_MATRIX_HH
+#ifndef cFitnessMatrix_h
+#define cFitnessMatrix_h
#include <numeric>
#include <iomanip>
@@ -17,25 +20,25 @@
#include <list>
#include <sys/timeb.h>
-#ifndef DEFS_HH
+#ifndef defs_h
#include "defs.h"
#endif
-#ifndef MX_CODE_ARRAY_HH
+#ifndef cMxCodeArray_h
#include "cMxCodeArray.h"
#endif
-#ifndef MY_CODE_ARRAY_LESS_THAN_HH
+#ifndef MyCodeArrayLessThan_h
#include "MyCodeArrayLessThan.h"
#endif
-#ifndef ORGANISM_HH
+#ifndef cOrganism_h
#include "cOrganism.h"
#endif
-#ifndef STATS_HH
+#ifndef cStats_h
#include "cStats.h"
#endif
-#ifndef STRING_UTIL_HH
+#ifndef cStringUtil_h
#include "cStringUtil.h"
#endif
-#ifndef TOOLS_HH
+#ifndef cTools_h
#include "cTools.h"
#endif
Modified: development/source/main/cGenome.cc
===================================================================
--- development/source/main/cGenome.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cGenome.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2001 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cGenome.cc
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
#include "cGenome.h"
@@ -11,10 +14,6 @@
using namespace std;
-/////////////
-// cGenome
-/////////////
-
cGenome::cGenome(int _size)
: genome(_size), active_size(_size)
{
Modified: development/source/main/cGenome.h
===================================================================
--- development/source/main/cGenome.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cGenome.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,22 +1,25 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cGenome.h
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef GENOME_HH
-#define GENOME_HH
+#ifndef cGenome_h
+#define cGenome_h
#include <assert.h>
-#ifndef INSTRUCTION_HH
+#ifndef cInstruction_h
#include "cInstruction.h"
#endif
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
-#ifndef TARRAY_HH
+#ifndef tArray_h
#include "tArray.h"
#endif
Modified: development/source/main/cGenomeUtil.cc
===================================================================
--- development/source/main/cGenomeUtil.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cGenomeUtil.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2001 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cGenomeUtil.cc
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
#include "cGenomeUtil.h"
Modified: development/source/main/cGenomeUtil.h
===================================================================
--- development/source/main/cGenomeUtil.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cGenomeUtil.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,18 +1,22 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cGenomeUtil.h
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef GENOME_UTIL_HH
-#define GENOME_UTIL_HH
+#ifndef cGenomeUtil_h
+#define cGenomeUtil_h
-#ifndef GENOME_HH
+#ifndef cGenome_h
#include "cGenome.h"
#endif
class cInstruction;
+
class cGenomeUtil {
public:
// ========= Detection =========
Modified: development/source/main/cInstLibBase.h
===================================================================
--- development/source/main/cInstLibBase.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cInstLibBase.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,18 +1,22 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cGenomeUtil.h
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef INST_LIB_BASE_HH
-#define INST_LIB_BASE_HH
+#ifndef cInstLibBase_h
+#define cInstLibBase_h
-#ifndef INSTRUCTION_HH
+#ifndef cInstruction_h
#include "cInstruction.h"
#endif
class cString;
+
class cInstLibBase {
public:
virtual ~cInstLibBase() { ; }
Modified: development/source/main/cInstSet.cc
===================================================================
--- development/source/main/cInstSet.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cInstSet.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2001 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cInstSet.cc
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2001 California Institute of Technology.
+ *
+ */
#include "cInstSet.h"
Modified: development/source/main/cInstSet.h
===================================================================
--- development/source/main/cInstSet.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cInstSet.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,25 +1,28 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cInstSet.h
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2001 California Institute of Technology.
+ *
+ */
#ifndef cInstSet_h
#define cInstSet_h
#include <iostream>
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
-#ifndef TARRAY_HH
+#ifndef tArray_h
#include "tArray.h"
#endif
-#ifndef INSTRUCTION_HH
+#ifndef cInstruction_h
#include "cInstruction.h"
#endif
-#ifndef INST_LIB_BASE_HH
+#ifndef cInstLibBase_h
#include "cInstLibBase.h"
#endif
Modified: development/source/main/cInstUtil.cc
===================================================================
--- development/source/main/cInstUtil.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cInstUtil.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cInstUtil.cc
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
#include "cInstUtil.h"
Modified: development/source/main/cInstUtil.h
===================================================================
--- development/source/main/cInstUtil.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cInstUtil.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,16 +1,19 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cInstUtil.h
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef INST_UTIL_HH
-#define INST_UTIL_HH
+#ifndef cInstUtil_h
+#define cInstUtil_h
#include <iostream>
-#ifndef GENOME_HH
+#ifndef cGenome_h
#include "cGenome.h"
#endif
Modified: development/source/main/cInstruction.cc
===================================================================
--- development/source/main/cInstruction.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cInstruction.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2001 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cInstruction.cc
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
#include "cInstruction.h"
Modified: development/source/main/cInstruction.h
===================================================================
--- development/source/main/cInstruction.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cInstruction.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,22 +1,25 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cInstruction.h
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef INSTRUCTION_HH
-#define INSTRUCTION_HH
+#ifndef cInstruction_h
+#define cInstruction_h
#include <assert.h>
-#ifndef DEFS_HH
+#ifndef defs_h
#include "defs.h"
#endif
class cInstruction {
private:
- UCHAR operand;
+ unsigned char operand;
public:
// Accessors...
Modified: development/source/main/cLandscape.cc
===================================================================
--- development/source/main/cLandscape.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cLandscape.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2001 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cLandscape.cc
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
#include "cLandscape.h"
@@ -21,10 +24,6 @@
using namespace std;
-////////////////
-// cLandscape
-////////////////
-
cLandscape::cLandscape(cWorld* world, const cGenome & in_genome, const cInstSet & in_inst_set)
: m_world(world), inst_set(in_inst_set), base_genome(1), peak_genome(1)
{
Modified: development/source/main/cLandscape.h
===================================================================
--- development/source/main/cLandscape.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cLandscape.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cLandscape.h
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
#ifndef cLandscape_h
#define cLandscape_h
@@ -24,9 +27,6 @@
#include <fstream>
class cInstSet;
-class cGenome; // aggregate
-class cCPUTestInfo; // aggregate
-template <class T> class tMatrix; // aggregate
class cInstruction;
class cWorld;
Modified: development/source/main/cLocalMutations.cc
===================================================================
--- development/source/main/cLocalMutations.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cLocalMutations.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,27 +1,19 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cLocalMutations.cc
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef LOCAL_MUTATIONS_HH
#include "cLocalMutations.h"
-#endif
-#ifndef MUTATION_HH
#include "cMutation.h"
-#endif
-#ifndef MUTATION_LIB_HH
#include "cMutationLib.h"
-#endif
-#ifndef nMutation_h
#include "nMutation.h"
-#endif
-/////////////////////
-// cLocalMutations
-/////////////////////
cLocalMutations::cLocalMutations(const cMutationLib & _lib, int genome_length)
: mut_lib(_lib)
Modified: development/source/main/cLocalMutations.h
===================================================================
--- development/source/main/cLocalMutations.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cLocalMutations.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,14 +1,17 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cLocalMutations.h
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef LOCAL_MUTATIONS_HH
-#define LOCAL_MUTATIONS_HH
+#ifndef cLocalMutations_h
+#define cLocalMutations_h
-#ifndef TARRAY_HH
+#ifndef tArray_h
#include "tArray.h"
#endif
Deleted: development/source/main/cMutation.cc
===================================================================
--- development/source/main/cMutation.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cMutation.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,30 +0,0 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
-
-#ifndef MUTATION_HH
-#include "cMutation.h"
-#endif
-
-
-///////////////
-// cMutation
-///////////////
-
-cMutation::cMutation(const cString & _name, int _id, int _trigger,
- int _scope, int _type, double _rate)
- : name(_name)
- , id(_id)
- , trigger(_trigger)
- , scope(_scope)
- , type(_type)
- , rate(_rate)
-{
-}
-
-cMutation::~cMutation()
-{
-}
Modified: development/source/main/cMutation.h
===================================================================
--- development/source/main/cMutation.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cMutation.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,14 +1,17 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cMutation.h
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef MUTATION_HH
-#define MUTATION_HH
+#ifndef cMutation_h
+#define cMutation_h
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
@@ -21,9 +24,11 @@
int type;
double rate;
public:
- cMutation(const cString & _name, int _id, int _trigger, int _scope,
- int _type, double _rate);
- ~cMutation();
+ cMutation(const cString & _name, int _id, int _trigger, int _scope, int _type, double _rate)
+ : name(_name), id(_id), trigger(_trigger), scope(_scope), type(_type), rate(_rate)
+ {
+ }
+ ~cMutation() { ; }
const cString & GetName() const { return name; }
int GetID() const { return id; }
Modified: development/source/main/cMutationLib.cc
===================================================================
--- development/source/main/cMutationLib.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cMutationLib.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,24 +1,18 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cMutationLib.cc
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef MUTATION_LIB_HH
#include "cMutationLib.h"
-#endif
-#ifndef MUTATION_HH
#include "cMutation.h"
-#endif
-#ifndef nMutation_h
#include "nMutation.h"
-#endif
-//////////////////
-// cMutationLib
-//////////////////
cMutationLib::cMutationLib()
: trigger_list_array(nMutation::NUM_TRIGGERS)
Modified: development/source/main/cMutationLib.h
===================================================================
--- development/source/main/cMutationLib.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cMutationLib.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,22 +1,26 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cMutationLib.h
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef MUTATION_LIB_HH
-#define MUTATION_LIB_HH
+#ifndef cMutationLib_h
+#define cMutationLib_h
-#ifndef TARRAY_HH
+#ifndef tArray_h
#include "tArray.h"
#endif
-#ifndef TLIST_HH
+#ifndef tList_h
#include "tList.h"
#endif
class cMutation;
class cString;
+
class cMutationLib {
private:
tArray<cMutation *> mutation_array;
Modified: development/source/main/cMutationRates.cc
===================================================================
--- development/source/main/cMutationRates.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cMutationRates.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,28 +1,18 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cMutationRates.cc
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
#include "cMutationRates.h"
#include "cWorld.h"
-cMutationRates::cMutationRates(cWorld* world) : m_world(world)
-{
- Clear();
-}
-cMutationRates::cMutationRates(const cMutationRates & in_muts) : m_world(in_muts.m_world)
-{
- Copy(in_muts);
-}
-
-cMutationRates::~cMutationRates()
-{
-}
-
void cMutationRates::Clear()
{
exec.point_mut_prob = 0.0;
Modified: development/source/main/cMutationRates.h
===================================================================
--- development/source/main/cMutationRates.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cMutationRates.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,12 +1,15 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cMutationRates.h
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef MUTATION_RATES_HH
-#define MUTATION_RATES_HH
+#ifndef cMutationRates_h
+#define cMutationRates_h
class cWorld;
@@ -45,9 +48,9 @@
void operator=(const cMutationRates & in_muts)
{ (void) in_muts; } // Disable operator=
public:
- cMutationRates(cWorld* world);
- cMutationRates(const cMutationRates & in_muts);
- ~cMutationRates();
+ cMutationRates(cWorld* world) : m_world(world) { Clear(); }
+ cMutationRates(const cMutationRates & in_muts) : m_world(in_muts.m_world) { Copy(in_muts); }
+ ~cMutationRates() { ; }
void Clear();
void Copy(const cMutationRates & in_muts);
Modified: development/source/main/cMxCodeArray.cc
===================================================================
--- development/source/main/cMxCodeArray.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cMxCodeArray.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cMxCodeArray.cc
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
#include "cMxCodeArray.h"
Modified: development/source/main/cMxCodeArray.h
===================================================================
--- development/source/main/cMxCodeArray.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cMxCodeArray.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,25 +1,28 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cMxCodeArray.h
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef MX_CODE_ARRAY_HH
-#define MX_CODE_ARRAY_HH
+#ifndef cMxCodeArray_h
+#define cMxCodeArray_h
#include <iostream>
#include <list>
#include <map>
#include <set>
-#ifndef INSTRUCTION_HH
+#ifndef cInstruction_h
#include "cInstruction.h"
#endif
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
-#ifndef STRING_UTIL_HH
+#ifndef cStringUtil_h
#include "cStringUtil.h"
#endif
Modified: development/source/main/cOrgMessage.cc
===================================================================
--- development/source/main/cOrgMessage.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cOrgMessage.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,5 +1,15 @@
+/*
+ * cOrgMessage.cc
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
+
#include "cOrgMessage.h"
-#include <string>
+
#include <sstream>
void cOrgMessage::SetData(int in_data)
Modified: development/source/main/cOrgMessage.h
===================================================================
--- development/source/main/cOrgMessage.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cOrgMessage.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,12 +1,15 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cOrgMessage.h
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef ORG_MESSAGE_HH
-#define ORG_MESSAGE_HH
+#ifndef cOrgMessage_h
+#define cOrgMessage_h
#include <string>
Modified: development/source/main/cOrganism.cc
===================================================================
--- development/source/main/cOrganism.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cOrganism.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cOrganism.cc
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
#include "cOrganism.h"
@@ -26,9 +29,6 @@
using namespace std;
-///////////////
-// cOrganism
-///////////////
cOrganism::cOrganism(cWorld* world, const cGenome & in_genome)
: m_world(world)
Modified: development/source/main/cOrganism.h
===================================================================
--- development/source/main/cOrganism.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cOrganism.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,38 +1,41 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cOrganism.h
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef ORGANISM_HH
-#define ORGANISM_HH
+#ifndef cOrganism_h
+#define cOrganism_h
#include <fstream>
#include <deque>
-#ifndef CPU_MEMORY_HH
+#ifndef cCPUMemory_h
#include "cCPUMemory.h"
#endif
-#ifndef CPU_STATS_HH
+#ifndef sCPUStats_h
#include "sCPUStats.h"
#endif
-#ifndef GENOME_HH
+#ifndef cGenome_h
#include "cGenome.h"
#endif
-#ifndef LOCAL_MUTATIONS_HH
+#ifndef cLocalMutations_h
#include "cLocalMutations.h"
#endif
-#ifndef MUTATION_RATES_HH
+#ifndef cMutationRates_h
#include "cMutationRates.h"
#endif
-#ifndef PHENOTYPE_HH
+#ifndef cPhenotype_h
#include "cPhenotype.h"
#endif
-#ifndef POPULATION_INTERFACE_HH
+#ifndef cPopulationInterface_h
#include "cPopulationInterface.h"
#endif
-#ifndef TBUFFER_HH
+#ifndef tBuffer_h
#include "tBuffer.h"
#endif
@@ -43,19 +46,10 @@
class cHardwareBase;
class cGenotype;
-class cPhenotype; // aggregate
-class cGenome; // aggregate
class cInjectGenotype;
-class cMutationRates; // aggregate
-class cLocalMutations; // aggregate
-class cPopulationInterface; // aggregate
-class cCPUMemory; // aggregate
-class sCPUStats; // aggregate
class cLineage;
-template <class T> class tBuffer; // aggregate
class cOrgMessage;
class cEnvironment;
-class cOrganism;
class cCodeLabel;
class cOrganism {
Modified: development/source/main/cPhenotype.cc
===================================================================
--- development/source/main/cPhenotype.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cPhenotype.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cPhenotype.cc
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
#include "cPhenotype.h"
Modified: development/source/main/cPhenotype.h
===================================================================
--- development/source/main/cPhenotype.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cPhenotype.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,22 +1,25 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2004 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cPhenotype.h
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef PHENOTYPE_HH
-#define PHENOTYPE_HH
+#ifndef cPhenotype_h
+#define cPhenotype_h
#include <fstream>
-#ifndef MERIT_HH
+#ifndef cMerit_h
#include "cMerit.h"
#endif
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
-#ifndef TARRAY_HH
+#ifndef tArray_h
#include "tArray.h"
#endif
@@ -48,9 +51,6 @@
*************************************************************************/
class cEnvironment;
-class cMerit; // aggregate
-template <class T> class tArray; // aggregate
-class cString; // aggregate
template <class T> class tBuffer;
template <class T> class tList;
class cWorld;
Modified: development/source/main/cPopulation.cc
===================================================================
--- development/source/main/cPopulation.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cPopulation.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cPopulation.cc
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
#include "cPopulation.h"
Modified: development/source/main/cPopulation.h
===================================================================
--- development/source/main/cPopulation.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cPopulation.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,22 +1,25 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cPopulation.h
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef POPULATION_HH
-#define POPULATION_HH
+#ifndef cPopulation_h
+#define cPopulation_h
#include <fstream>
-#ifndef BIRTH_CHAMBER_HH
+#ifndef cBirthChamber_h
#include "cBirthChamber.h"
#endif
-#ifndef POPULATION_INTERFACE_HH
+#ifndef cPopulationInterface_h
#include "cPopulationInterface.h"
#endif
-#ifndef RESOURCE_COUNT_HH
+#ifndef cResourceCount_h
#include "cResourceCount.h"
#endif
#ifndef cString_h
@@ -25,28 +28,21 @@
#ifndef cWorld_h
#include "cWorld.h"
#endif
-#ifndef TARRAY_HH
+#ifndef tArray_h
#include "tArray.h"
#endif
-#ifndef TLIST_HH
+#ifndef tList_h
#include "tList.h"
#endif
class cSchedule;
-template <class T> class tArray; // aggregate
-
-class cBirthChamber; // aggregate
class cChangeList;
class cEnvironment;
class cGenome;
class cGenotype;
class cLineage;
-template <class T> class tList; // aggregate
class cOrganism;
-class cPopulationInterface; // aggregate
class cPopulationCell;
-class cResourceCount; // aggregate
-class cString; // aggregate
class cPopulation {
private:
Modified: development/source/main/cPopulationCell.cc
===================================================================
--- development/source/main/cPopulationCell.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cPopulationCell.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cPopulationCell.cc
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
#include "cPopulationCell.h"
@@ -13,6 +16,7 @@
using namespace std;
+
cPopulationCell::cPopulationCell()
: m_world(NULL)
, organism(NULL)
Modified: development/source/main/cPopulationCell.h
===================================================================
--- development/source/main/cPopulationCell.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cPopulationCell.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,31 +1,31 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cPopulationCell.h
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef POPULATION_CELL_HH
-#define POPULATION_CELL_HH
+#ifndef cPopulationCell_h
+#define cPopulationCell_h
#include <fstream>
-#ifndef MUTATION_RATES_HH
+#ifndef cMutationRates_h
#include "cMutationRates.h"
#endif
-#ifndef TARRAY_HH
+#ifndef tArray_h
#include "tArray.h"
#endif
-#ifndef TLIST_HH
+#ifndef tList_h
#include "tList.h"
#endif
class cPopulation;
class cOrganism;
-template <class T> class tList; // aggregate
class cPopulationCell;
-class cMutationRates; // aggregate
-template <class T> class tArray; // aggregate
class cPopulationCell {
friend class cPopulation;
Modified: development/source/main/cPopulationInterface.cc
===================================================================
--- development/source/main/cPopulationInterface.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cPopulationInterface.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cPopulationInterface.cc
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
#include "cPopulationInterface.h"
@@ -22,6 +25,7 @@
#define NULL 0
#endif
+
cHardwareBase* cPopulationInterface::NewHardware(cOrganism * owner)
{
return m_world->GetHardwareManager().Create(owner);
Modified: development/source/main/cPopulationInterface.h
===================================================================
--- development/source/main/cPopulationInterface.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cPopulationInterface.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,15 +1,16 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cPopulationInterface.h
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-// This class is used by organisms to interface with their population.
+#ifndef cPopulationInterface_h
+#define cPopulationInterface_h
-#ifndef POPULATION_INTERFACE_HH
-#define POPULATION_INTERFACE_HH
-
#include "cWorld.h"
#include "cAvidaDriver_Base.h"
Modified: development/source/main/cReaction.cc
===================================================================
--- development/source/main/cReaction.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cReaction.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,26 +1,20 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2001 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cReaction.cc
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2001 California Institute of Technology.
+ *
+ */
-#ifndef REACTION_HH
#include "cReaction.h"
-#endif
-#ifndef REACTION_PROCESS_HH
#include "cReactionProcess.h"
-#endif
-#ifndef REACTION_REQUISITE_HH
#include "cReactionRequisite.h"
-#endif
using namespace std;
-///////////////
-// cReaction
-///////////////
cReaction::cReaction(const cString & _name, int _id)
: name(_name)
Modified: development/source/main/cReaction.h
===================================================================
--- development/source/main/cReaction.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cReaction.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,23 +1,24 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2004 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cReaction.h
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2004 California Institute of Technology.
+ *
+ */
-#ifndef REACTION_HH
-#define REACTION_HH
+#ifndef cReaction_h
+#define cReaction_h
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
-#ifndef TLIST_HH
+#ifndef tList_h
#include "tList.h"
#endif
-class cString; // aggregate
class cTaskEntry;
-template <class T> class tList; // aggregate
class cReactionProcess;
class cReactionRequisite;
Modified: development/source/main/cReactionLib.cc
===================================================================
--- development/source/main/cReactionLib.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cReactionLib.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,21 +1,17 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2001 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cReactionLib.cc
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2001 California Institute of Technology.
+ *
+ */
-#ifndef REACTION_LIB_HH
#include "cReactionLib.h"
-#endif
-#ifndef REACTION_HH
#include "cReaction.h"
-#endif
-//////////////////
-// cReactionLib
-//////////////////
cReactionLib::~cReactionLib()
{
Modified: development/source/main/cReactionLib.h
===================================================================
--- development/source/main/cReactionLib.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cReactionLib.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,14 +1,17 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2001 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cReactionLib.h
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2001 California Institute of Technology.
+ *
+ */
-#ifndef REACTION_LIB_HH
-#define REACTION_LIB_HH
+#ifndef cReactionLib_h
+#define cReactionLib_h
-#ifndef TARRAY_HH
+#ifndef tArray_h
#include "tArray.h"
#endif
Deleted: development/source/main/cReactionProcess.cc
===================================================================
--- development/source/main/cReactionProcess.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cReactionProcess.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,38 +0,0 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2001 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
-
-#ifndef REACTION_PROCESS_HH
-#include "cReactionProcess.h"
-#endif
-
-#ifndef DEFS_HH
-#include "defs.h"
-#endif
-#ifndef nReaction_h
-#include "nReaction.h"
-#endif
-
-//////////////////////
-// cReactionProcess
-//////////////////////
-
-cReactionProcess::cReactionProcess()
- : resource(NULL)
- , value(1.0)
- , type(nReaction::PROCTYPE_ADD)
- , max_number(1.0)
- , min_number(0.0)
- , max_fraction(1.0)
- , product(NULL)
- , conversion(1.0)
- , lethal(0)
- , inst_id(-1)
- , detect(NULL)
- , detection_threshold(0.0)
- , detection_error(0.0)
-{
-}
Modified: development/source/main/cReactionProcess.h
===================================================================
--- development/source/main/cReactionProcess.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cReactionProcess.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,21 +1,32 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2004 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cReactionProcess.h
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2004 California Institute of Technology.
+ *
+ */
-#ifndef REACTION_PROCESS_HH
-#define REACTION_PROCESS_HH
+#ifndef cReactionProcess_h
+#define cReactionProcess_h
+#ifndef defs_h
+#include "defs.h"
+#endif
+#ifndef nReaction_h
+#include "nReaction.h"
+#endif
+
#include <iostream>
using namespace std;
class cResource;
+
class cReactionProcess {
private:
- cResource * resource; // Resource consumed.
+ cResource* resource; // Resource consumed.
double value; // Efficiency.
int type; // Method of applying bonuses.
double max_number; // Max quantity of resource usable.
@@ -31,7 +42,22 @@
double detection_threshold; // Min quantity of resource to register present
double detection_error; // Var of Detection Event (as % of resource present)
public:
- cReactionProcess();
+ cReactionProcess()
+ : resource(NULL)
+ , value(1.0)
+ , type(nReaction::PROCTYPE_ADD)
+ , max_number(1.0)
+ , min_number(0.0)
+ , max_fraction(1.0)
+ , product(NULL)
+ , conversion(1.0)
+ , lethal(0)
+ , inst_id(-1)
+ , detect(NULL)
+ , detection_threshold(0.0)
+ , detection_error(0.0)
+ {
+ }
~cReactionProcess() { ; }
cResource * GetResource() const { return resource; }
Deleted: development/source/main/cReactionRequisite.cc
===================================================================
--- development/source/main/cReactionRequisite.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cReactionRequisite.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,26 +0,0 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2001 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
-
-#ifndef REACTION_REQUISITE_HH
-#include "cReactionRequisite.h"
-#endif
-
-#include <limits.h>
-
-////////////////////////
-// cReactionRequisite
-////////////////////////
-
-cReactionRequisite::cReactionRequisite()
- : min_task_count(0)
- , max_task_count(INT_MAX)
-{
-}
-
-cReactionRequisite::~cReactionRequisite()
-{
-}
Modified: development/source/main/cReactionRequisite.h
===================================================================
--- development/source/main/cReactionRequisite.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cReactionRequisite.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,18 +1,22 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2001 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cReactionRequisite.h
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2001 California Institute of Technology.
+ *
+ */
-#ifndef REACTION_REQUISITE_HH
-#define REACTION_REQUISITE_HH
+#ifndef cReactionRequisite_h
+#define cReactionRequisite_h
-#ifndef TLIST_HH
+#ifndef tList_h
#include "tList.h"
#endif
class cReaction;
+
class cReactionRequisite {
private:
tList<cReaction> prior_reaction_list;
@@ -23,8 +27,8 @@
// disabled copy constructor.
cReactionRequisite(const cReactionRequisite &);
public:
- cReactionRequisite();
- ~cReactionRequisite();
+ cReactionRequisite() : min_task_count(0) , max_task_count(INT_MAX) { ; }
+ ~cReactionRequisite() { ; }
const tList<cReaction> & GetReactions() const { return prior_reaction_list; }
const tList<cReaction> & GetNoReactions() const
Modified: development/source/main/cReactionResult.cc
===================================================================
--- development/source/main/cReactionResult.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cReactionResult.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2004 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cReactionResult.cc
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2004 California Institute of Technology.
+ *
+ */
#include "cReactionResult.h"
Modified: development/source/main/cReactionResult.h
===================================================================
--- development/source/main/cReactionResult.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cReactionResult.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,19 +1,20 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2004 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cReactionResult.h
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2004 California Institute of Technology.
+ *
+ */
-#ifndef REACTION_RESULT_HH
-#define REACTION_RESULT_HH
+#ifndef cReactionResult_h
+#define cReactionResult_h
-#ifndef TARRAY_HH
+#ifndef tArray_h
#include "tArray.h"
#endif
-template <class T> class tArray; // aggregate
-
class cReactionResult {
private:
tArray<double> resources_consumed;
Modified: development/source/main/cResource.cc
===================================================================
--- development/source/main/cResource.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cResource.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2001 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cResource.cc
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2001 California Institute of Technology.
+ *
+ */
#include "cResource.h"
@@ -11,6 +14,7 @@
using namespace std;
+
cResource::cResource(const cString & _name, int _id)
: name(_name)
, id(_id)
Modified: development/source/main/cResource.h
===================================================================
--- development/source/main/cResource.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cResource.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,19 +1,20 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cResource.h
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef RESOURCE_HH
-#define RESOURCE_HH
+#ifndef cResource_h
+#define cResource_h
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
-class cString; // aggregate
-
class cResource {
private:
cString name;
Modified: development/source/main/cResourceCount.cc
===================================================================
--- development/source/main/cResourceCount.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cResourceCount.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2001 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cResourceCount.cc
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2001 California Institute of Technology.
+ *
+ */
#include "cResourceCount.h"
@@ -19,6 +22,7 @@
const double cResourceCount::EPSILON (1.0e-15);
const int cResourceCount::PRECALC_DISTANCE(100);
+
void FlowMatter(cSpatialCountElem &elem1, cSpatialCountElem &elem2, double inxdiffuse,
double inydiffuse, double inxgravity, double inygravity,
int xdist, int ydist, double dist) {
Modified: development/source/main/cResourceCount.h
===================================================================
--- development/source/main/cResourceCount.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cResourceCount.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,31 +1,29 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2001 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cResourceCount.h
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2001 California Institute of Technology.
+ *
+ */
-#ifndef RESOURCE_COUNT_HH
-#define RESOURCE_COUNT_HH
+#ifndef cResourceCount_h
+#define cResourceCount_h
-#ifndef SPATIAL_RES_COUNT_HH
+#ifndef cSpatialResCount_h
#include "cSpatialResCount.h"
#endif
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
-#ifndef TARRAY_HH
+#ifndef tArray_h
#include "tArray.h"
#endif
-#ifndef TMATRIX_HH
+#ifndef tMatrix_h
#include "tMatrix.h"
#endif
-template <class T> class tArray; // aggregate
-template <class T> class tMatrix; // aggregate
-class cSpatialResCount; // aggregate
-class cString; // aggregate
-
class cResourceCount {
private:
mutable tArray<double> resource_count; // Current quantity of each resource
Modified: development/source/main/cResourceLib.cc
===================================================================
--- development/source/main/cResourceLib.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cResourceLib.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,20 +1,20 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cResourceLib.cc
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef RESOURCE_LIB_HH
#include "cResourceLib.h"
-#endif
-#ifndef RESOURCE_HH
#include "cResource.h"
-#endif
using namespace std;
+
cResourceLib::~cResourceLib()
{
for (int i = 0; i < resource_array.GetSize(); i++) {
Modified: development/source/main/cResourceLib.h
===================================================================
--- development/source/main/cResourceLib.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cResourceLib.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,19 +1,23 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cResourceLib.h
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef RESOURCE_LIB_HH
-#define RESOURCE_LIB_HH
+#ifndef cResourceLib_h
+#define cResourceLib_h
-#ifndef TARRAY_HH
+#ifndef tArray_h
#include "tArray.h"
#endif
class cResource;
class cString;
+
class cResourceLib {
private:
tArray<cResource *> resource_array;
Modified: development/source/main/cSpatialCountElem.cc
===================================================================
--- development/source/main/cSpatialCountElem.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cSpatialCountElem.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,16 +1,18 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2001 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cSpatialCountElem.cc
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2001 California Institute of Technology.
+ *
+ */
-#ifndef SPATIAL_COUNT_ELEM_HH
#include "cSpatialCountElem.h"
-#endif
const int MAXFLOWPTS = 8;
+
cSpatialCountElem::cSpatialCountElem (double initamount) {
amount = initamount;
delta=0.0;
Modified: development/source/main/cSpatialCountElem.h
===================================================================
--- development/source/main/cSpatialCountElem.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cSpatialCountElem.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,14 +1,17 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2001 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cSpatialCountElem.h
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2001 California Institute of Technology.
+ *
+ */
-#ifndef SPATIAL_COUNT_ELEM_HH
-#define SPATIAL_COUNT_ELEM_HH
+#ifndef cSpatialCountElem_h
+#define cSpatialCountElem_h
-#ifndef TARRAY_HH
+#ifndef tArray_h
#include "tArray.h"
#endif
Modified: development/source/main/cSpatialResCount.cc
===================================================================
--- development/source/main/cSpatialResCount.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cSpatialResCount.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,15 +1,19 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2001 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cSpatialResCount.cc
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2001 California Institute of Technology.
+ *
+ */
#include "cSpatialResCount.h"
#include "functions.h"
#include "nGeometry.h"
+
cSpatialResCount::cSpatialResCount(int inworld_x, int inworld_y,
int ingeometry,
double inxdiffuse, double inydiffuse, double inxgravity,
Modified: development/source/main/cSpatialResCount.h
===================================================================
--- development/source/main/cSpatialResCount.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cSpatialResCount.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,17 +1,20 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2001 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cSpatialResCount.h
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2001 California Institute of Technology.
+ *
+ */
-#ifndef SPATIAL_RES_COUNT_HH
-#define SPATIAL_RES_COUNT_HH
+#ifndef cSpatialResCount_h
+#define cSpatialResCount_h
-#ifndef SPATIAL_COUNT_ELEM_HH
+#ifndef cSpatialCountElem_h
#include "cSpatialCountElem.h"
#endif
-#ifndef TARRAY_HH
+#ifndef tArray_h
#include "tArray.h"
#endif
Modified: development/source/main/cStats.cc
===================================================================
--- development/source/main/cStats.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cStats.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2001 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cStats.cc
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2001 California Institute of Technology.
+ *
+ */
#include "cStats.h"
@@ -17,9 +20,6 @@
using namespace std;
-////////////
-// cStats
-////////////
cStats::cStats(cWorld* world)
: m_world(world)
Modified: development/source/main/cStats.h
===================================================================
--- development/source/main/cStats.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cStats.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,47 +1,46 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2002 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cStats.h
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2002 California Institute of Technology.
+ *
+ */
-#ifndef STATS_HH
-#define STATS_HH
+#ifndef cStats_h
+#define cStats_h
#include <assert.h>
#include <fstream>
#include <iostream>
-#ifndef DEFS_HH
+#ifndef defs_h
#include "defs.h"
#endif
-#ifndef DOUBLE_SUM_HH
+#ifndef cDoubleSum_h
#include "cDoubleSum.h"
#endif
-#ifndef FUNCTIONS_HH
+#ifndef functions_h
#include "functions.h"
#endif
-#ifndef INT_SUM_HH
+#ifndef cIntSum_h
#include "cIntSum.h"
#endif
-#ifndef RUNNING_AVERAGE_HH
+#ifndef cRunningAverage_h
#include "cRunningAverage.h"
#endif
-#ifndef TARRAY_HH
+#ifndef tArray_h
#include "tArray.h"
#endif
-#ifndef TDATAMANAGER_HH
+#ifndef tDataManager_h
#include "tDataManager.h"
#endif
+#ifndef nGeometry_h
#include "nGeometry.h"
+#endif
-template <class T> class tDataManager; // aggregate
-class cDoubleSum; // aggregate
-class cRunningAverage; // aggregate
-class cIntSum; // aggregate
-template <class T> class tArray; // aggregate
class cGenotype;
-class cString; // aggregate
class cInjectGenotype;
class cWorld;
Deleted: development/source/main/cTaskEntry.cc
===================================================================
--- development/source/main/cTaskEntry.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cTaskEntry.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,27 +0,0 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
-
-#ifndef TASK_ENTRY_HH
-#include "cTaskEntry.h"
-#endif
-
-////////////////
-// cTaskEntry
-////////////////
-
-cTaskEntry::cTaskEntry(const cString & _name, const cString & _desc,
- int _id, tTaskTest _test_fun)
- : name(_name)
- , desc(_desc)
- , id(_id)
- , test_fun(_test_fun)
-{
-}
-
-cTaskEntry::~cTaskEntry()
-{
-}
Modified: development/source/main/cTaskEntry.h
===================================================================
--- development/source/main/cTaskEntry.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cTaskEntry.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,17 +1,20 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cTaskEntry.h
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef TASK_ENTRY_HH
-#define TASK_ENTRY_HH
+#ifndef cTaskEntry_h
+#define cTaskEntry_h
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
-#ifndef TASK_LIB_HH
+#ifndef cTaskLib_h
#include "cTaskLib.h"
#endif
@@ -22,9 +25,11 @@
int id;
tTaskTest test_fun;
public:
- cTaskEntry(const cString & _name, const cString & _desc, int _id,
- tTaskTest _test_fun);
- ~cTaskEntry();
+ cTaskEntry(const cString & _name, const cString & _desc, int _id, tTaskTest _test_fun)
+ : name(_name), desc(_desc), id(_id), test_fun(_test_fun)
+ {
+ }
+ ~cTaskEntry() { ; }
const cString & GetName() const { return name; }
const cString & GetDesc() const { return desc; }
Modified: development/source/main/cTaskLib.cc
===================================================================
--- development/source/main/cTaskLib.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cTaskLib.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,17 +1,16 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cTaskLib.cc
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef TASK_LIB_HH
#include "cTaskLib.h"
-#endif
-#ifndef TASK_ENTRY_HH
#include "cTaskEntry.h"
-#endif
extern "C" {
#include <math.h>
@@ -20,9 +19,6 @@
using namespace std;
-////////////////////////
-// cTaskLib (public)
-////////////////////////
cTaskLib::cTaskLib()
: use_neighbor_input(false)
Modified: development/source/main/cTaskLib.h
===================================================================
--- development/source/main/cTaskLib.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/main/cTaskLib.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,20 +1,23 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cTaskLib.h
+ * Avida
+ *
+ * Created by David on 12/5/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef TASK_LIB_HH
-#define TASK_LIB_HH
+#ifndef cTaskLib_h
+#define cTaskLib_h
-#ifndef TARRAY_HH
+#ifndef tArray_h
#include "tArray.h"
#endif
-#ifndef TBUFFER_HH
+#ifndef tBuffer_h
#include "tBuffer.h"
#endif
-#ifndef TLIST_HH
+#ifndef tList_h
#include "tList.h"
#endif
@@ -23,6 +26,7 @@
class cString;
class cTaskEntry;
+
class cTaskLib {
private:
tArray<cTaskEntry *> task_array;
Modified: development/source/tools/CMakeLists.txt
===================================================================
--- development/source/tools/CMakeLists.txt 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/CMakeLists.txt 2005-12-07 23:44:39 UTC (rev 414)
@@ -3,14 +3,12 @@
cChangeList.cc
cConstSchedule.cc
cCountTracker.cc
- cDataEntry.cc
cDataFile.cc
cDataFileManager.cc
cDataManager_Base.cc
cDefaultMessageDisplay.cc
cDoubleSum.cc
cFile.cc
- cFixedBlock.cc
cGenesis.cc
cHelpAlias.cc
cHelpManager.cc
@@ -25,9 +23,7 @@
cMerit.cc
cProbSchedule.cc
cRandom.cc
- cRefBlock.cc
cRunningAverage.cc
- cScaledBlock.cc
cSchedule.cc
cString.cc
cStringIterator.cc
Modified: development/source/tools/cBlockStruct.cc
===================================================================
--- development/source/tools/cBlockStruct.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cBlockStruct.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,21 +1,19 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2000 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cBlockStruct.cc
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef BLOCK_STRUCT_HH
#include "cBlockStruct.h"
-#endif
#include <iostream>
using namespace std;
-////////////////////
-// cBlockStruct
-////////////////////
cBlockStruct::cBlockStruct(int in_num_scaled, int in_num_fixed)
{
Modified: development/source/tools/cBlockStruct.h
===================================================================
--- development/source/tools/cBlockStruct.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cBlockStruct.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,23 +1,26 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cBlockStruct.h
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef BLOCK_STRUCT_HH
-#define BLOCK_STRUCT_HH
+#ifndef cBlockStruct_H
+#define cBlockStruct_h
-#ifndef FIXEDBLOCK_HH
+#ifndef cFixedBlock_h
#include "cFixedBlock.h"
#endif
-#ifndef FIXEDCOORDS_HH
+#ifndef cFixedCoords_h
#include "cFixedCoords.h"
#endif
-#ifndef SCALED_BLOCK_HH
+#ifndef cScaledBlock_h
#include "cScaledBlock.h"
#endif
-#ifndef UINT_HH
+#ifndef cUInt_h
#include "cUInt.h"
#endif
@@ -126,11 +129,6 @@
* recalculate the fixed_size every time it is run.
**/
-class cFixedCoords; // aggregate
-class cFixedBlock; // accessed
-class cScaledBlock; // accessed
-class cUInt; // aggregate
-
class cBlockStruct {
private:
cFixedBlock * fixed_array;
Modified: development/source/tools/cChangeList.cc
===================================================================
--- development/source/tools/cChangeList.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cChangeList.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2005 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cChangeList.cc
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2005 California Institute of Technology.
+ *
+ */
#include "cChangeList.h"
Modified: development/source/tools/cChangeList.h
===================================================================
--- development/source/tools/cChangeList.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cChangeList.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,14 +1,17 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2005 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cChangeList.h
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2005 California Institute of Technology.
+ *
+ */
-#ifndef CHANGE_LIST_HH
-#define CHANGE_LIST_HH
+#ifndef cChangeList_h
+#define cChangeList_h
-#ifndef TARRAY_HH
+#ifndef tArray_h
#include "tArray.h"
#endif
Modified: development/source/tools/cConstSchedule.cc
===================================================================
--- development/source/tools/cConstSchedule.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cConstSchedule.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cConstSchedule.cc
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
#include "cConstSchedule.h"
@@ -11,10 +14,6 @@
#include "cMerit.h"
-////////////////////
-// cConstSchedule
-////////////////////
-
cConstSchedule::cConstSchedule(int _item_count)
: cSchedule(_item_count), is_active(_item_count)
{
Modified: development/source/tools/cConstSchedule.h
===================================================================
--- development/source/tools/cConstSchedule.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cConstSchedule.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,17 +1,20 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cConstSchedule.h
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef CONST_SCHEDULE_HH
-#define CONST_SCHEDULE_HH
+#ifndef cConstSchedule_h
+#define cConstSchedule_h
-#ifndef SCHEDULE_HH
+#ifndef cSchedule_h
#include "cSchedule.h"
#endif
-#ifndef TARRAY_HH
+#ifndef tArray_h
#include "tArray.h"
#endif
@@ -20,7 +23,6 @@
**/
class cMerit;
-template <class T> class tArray; // aggregate;
class cConstSchedule : public cSchedule {
private:
Modified: development/source/tools/cCountTracker.cc
===================================================================
--- development/source/tools/cCountTracker.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cCountTracker.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,15 +1,15 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cCountTracker.cc
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef COUNT_TRACKER_HH
#include "cCountTracker.h"
-#endif
-// cCountTracker /////////////////////////////////////////////////////////////
void cCountTracker::Inc()
{
Modified: development/source/tools/cCountTracker.h
===================================================================
--- development/source/tools/cCountTracker.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cCountTracker.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,12 +1,15 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cCountTracker.h
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef COUNT_TRACKER_HH
-#define COUNT_TRACKER_HH
+#ifndef cCountTracker_h
+#define cCountTracker_h
class cCountTracker {
private:
Modified: development/source/tools/cCycleCheck.cc
===================================================================
--- development/source/tools/cCycleCheck.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cCycleCheck.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,10 +1,13 @@
/*
-Copyright (C) 1993 - 2004 California Institute of Technology
+ * cCycleCheck.cc
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2004 California Institute of Technology.
+ *
+ */
-Read the COPYING and README files, or contact 'avida at alife.org',
-before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE.
-*/
-
#include "cCycleCheck.h"
#include "cID.h"
Modified: development/source/tools/cCycleCheck.h
===================================================================
--- development/source/tools/cCycleCheck.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cCycleCheck.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,13 +1,16 @@
/*
-Copyright (C) 1993 - 2004 California Institute of Technology
+ * cCycleCheck.h
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2004 California Institute of Technology.
+ *
+ */
-Read the COPYING and README files, or contact 'avida at alife.org',
-before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE.
-*/
+#ifndef cCycleCheck_h
+#define cCycleCheck_h
-#ifndef CYCLE_CHECK_HH
-#define CYCLE_CHECK_HH
-
class cID;
/*!
Deleted: development/source/tools/cDataEntry.cc
===================================================================
--- development/source/tools/cDataEntry.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cDataEntry.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,17 +0,0 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
-
-#ifndef DATA_ENTRY_HH
-#include "cDataEntry.h"
-#endif
-
-
-std::ostream& operator << (std::ostream& out, cDataEntry & entry)
-{
- entry.Print(out);
- return out;
-}
Modified: development/source/tools/cDataEntry.h
===================================================================
--- development/source/tools/cDataEntry.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cDataEntry.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,21 +1,22 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cDataEntry.h
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef DATA_ENTRY_HH
-#define DATA_ENTRY_HH
+#ifndef cDataEntry_h
+#define cDataEntry_h
#include <iostream>
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
-class cString; // aggregate
-
class cDataEntry {
private:
cString name; // Short Name
@@ -38,6 +39,10 @@
virtual bool Print(std::ostream& fp) const { (void) fp; return false; }
};
-std::ostream& operator << (std::ostream& out, cDataEntry & entry);
+std::ostream& operator << (std::ostream& out, cDataEntry & entry)
+{
+ entry.Print(out);
+ return out;
+}
#endif
Modified: development/source/tools/cDataFile.cc
===================================================================
--- development/source/tools/cDataFile.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cDataFile.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,17 +1,16 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cDataFile.cc
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-#ifndef DATA_FILE_HH
#include "cDataFile.h"
-#endif
-#ifndef STRING_UTIL_HH
#include "cStringUtil.h"
-#endif
extern "C" {
#include <stdio.h>
@@ -20,6 +19,7 @@
using namespace std;
+
void cDataFile::Init()
{
m_descr_written = false;
Modified: development/source/tools/cDataFile.h
===================================================================
--- development/source/tools/cDataFile.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cDataFile.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,25 +1,19 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cDataFile.h
+ * Avida
+ *
+ * Created by David on 12/2/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology.
+ *
+ */
-/* cDataFile.h ****************************************************************
- cDataFile
+#ifndef cDataFile_h
+#define cDataFile_h
- charles at krl.caltech.edu & travc at ugcs.caltech.edu
- Time-stamp: <1999-01-07 10:02:09 travc>
-
- cString: basic string class
-******************************************************************************/
-
-#ifndef DATA_FILE_HH
-#define DATA_FILE_HH
-
#include <fstream>
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
@@ -29,8 +23,6 @@
* @ref cFile.
*/
-class cString; // aggregate
-
class cDataFile {
private:
Modified: development/source/tools/cDataFileManager.cc
===================================================================
--- development/source/tools/cDataFileManager.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cDataFileManager.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -12,6 +12,7 @@
using namespace std;
+
cDataFileManager::~cDataFileManager()
{
tList<cString> names;
Modified: development/source/tools/cDataManager_Base.cc
===================================================================
--- development/source/tools/cDataManager_Base.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cDataManager_Base.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2001 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cDataManager_Base.cc
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2001 California Institute of Technology
+ *
+ */
#include "cDataManager_Base.h"
@@ -11,6 +14,7 @@
using namespace std;
+
bool cDataManager_Base::PrintRow(cDataFile& data_file, cString row_entries, char sep)
{
bool result = true;
Modified: development/source/tools/cDataManager_Base.h
===================================================================
--- development/source/tools/cDataManager_Base.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cDataManager_Base.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,21 +1,23 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cDataManager_Base.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef DATA_MANAGER_BASE_HH
-#define DATA_MANAGER_BASE_HH
+#ifndef cDataManager_h
+#define cDataManager_h
#include <iostream>
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
class cDataFile;
-class cString; // aggregate
class cDataManager_Base {
private:
Modified: development/source/tools/cDefaultMessageDisplay.cc
===================================================================
--- development/source/tools/cDefaultMessageDisplay.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cDefaultMessageDisplay.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,23 +1,22 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cDefaultMessageDisplay.cc
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef DEFAULT_MESSAGE_DISPLAY_HH
#include "cDefaultMessageDisplay.h"
-#endif
-#ifndef STRING_HH
#include "cString.h"
-#endif
using namespace std;
-void cDefaultMessageDisplay::out(cString &final_msg)
-{ *_out << final_msg << endl; _out->flush(); }
+void cDefaultMessageDisplay::out(cString& final_msg) { *_out << final_msg << endl; _out->flush(); }
+
/*
default instantiations of cDefaultMessageDisplay...
*/
Modified: development/source/tools/cDefaultMessageDisplay.h
===================================================================
--- development/source/tools/cDefaultMessageDisplay.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cDefaultMessageDisplay.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,16 +1,19 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cDefaultMessageDisplay.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef DEFAULT_MESSAGE_DISPLAY_HH
-#define DEFAULT_MESSAGE_DISPLAY_HH
+#ifndef cDefaultMessageDisplay_h
+#define cDefaultMessageDisplay_h
#include <iostream>
-#ifndef MESSAGE_DISPLAY_HH
+#ifndef cMessageDisplay_h
#include "cMessageDisplay.h"
#endif
@@ -31,12 +34,12 @@
class cString;
-class cDefaultMessageDisplay : public cMessageDisplay{
+class cDefaultMessageDisplay : public cMessageDisplay {
private:
- std::ostream *_out;
+ std::ostream* _out;
public:
- cDefaultMessageDisplay(std::ostream *stream):_out(stream){}
- void out(cString &final_msg);
+ cDefaultMessageDisplay(std::ostream* stream):_out(stream){}
+ void out(cString& final_msg);
};
extern cDefaultMessageDisplay s_info_msg_cout;
Modified: development/source/tools/cDoubleSum.cc
===================================================================
--- development/source/tools/cDoubleSum.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cDoubleSum.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,14 +1,14 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cDoubleSum.cc
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef DOUBLE_SUM_HH
#include "cDoubleSum.h"
-#endif
-// cDoubleSum ////////////////////////////////////////////////////////////////
const double cDoubleSum::INF_ERR = 0;
Modified: development/source/tools/cDoubleSum.h
===================================================================
--- development/source/tools/cDoubleSum.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cDoubleSum.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,12 +1,15 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cDoubleSum.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef DOUBLE_SUM_HH
-#define DOUBLE_SUM_HH
+#ifndef cDoubleSum_h
+#define cDoubleSum_h
#include <math.h>
#include <limits.h>
Modified: development/source/tools/cFile.cc
===================================================================
--- development/source/tools/cFile.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cFile.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,28 +1,15 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cFile.cc
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef FILE_HH
#include "cFile.h"
-#endif
-#ifndef INIT_FILE_HH
-#include "cInitFile.h"
-#endif
-#ifndef GENESIS_HH
-#include "cGenesis.h"
-#endif
-#ifndef STRING_ITERATOR_HH
-#include "cStringIterator.h"
-#endif
-
-#ifndef TOOLS_HH
-#include "cTools.h" // for g_debug global
-#endif
-
#include <iostream>
extern "C" {
@@ -30,18 +17,9 @@
#include <errno.h> // needed for FOPEN error constants (MSVC)
}
-
using namespace std;
-////////////
-// cFile
-////////////
-
-
-
-//bool cFile::Open(cString _fname, int flags)
-// porting to gcc 3.1 -- k
bool cFile::Open(cString _fname, ios::openmode flags)
{
if( IsOpen() ) Close(); // If a file is already open, clost it first.
@@ -65,8 +43,7 @@
else if (err_id == ENOENT) error_desc = "File or path not found";
// Print the error.
- cerr << "Unable to open file '" << _fname
- << "' : " << error_desc << endl;
+ cerr << "Unable to open file '" << _fname << "' : " << error_desc << endl;
return false;
}
@@ -97,20 +74,3 @@
in_string = cur_line;
return true;
}
-
-/*
-int cFile::CountLines()
-{
- char cur_line[MAX_STRING_LENGTH];
-
- Rewind();
- int n_lines = -1;
-
- do{
- fp.getline(cur_line, MAX_STRING_LENGTH);
- n_lines++;
- } while( cur_line[0]!='\0' && !fp.eof() );
-
- return n_lines;
-}
-*/
Modified: development/source/tools/cFile.h
===================================================================
--- development/source/tools/cFile.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cFile.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,16 +1,19 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cFile.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef FILE_HH
-#define FILE_HH
+#ifndef cFile_h
+#define cFile_h
#include <fstream>
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
@@ -21,8 +24,6 @@
* Its main usage is for the class @ref cInitFile.
**/
-class cString; // aggregate
-
class cFile {
private:
cFile(const cFile &);
Deleted: development/source/tools/cFixedBlock.cc
===================================================================
--- development/source/tools/cFixedBlock.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cFixedBlock.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,24 +0,0 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
-
-#ifndef FIXED_BLOCK_HH
-#include "cFixedBlock.h"
-#endif
-
-////////////////////
-// cFixedBlock
-////////////////////
-
-cFixedBlock::cFixedBlock()
-{
- start_point = 0;
-}
-
-cFixedBlock::~cFixedBlock()
-{
-}
-
Modified: development/source/tools/cFixedBlock.h
===================================================================
--- development/source/tools/cFixedBlock.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cFixedBlock.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,12 +1,15 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cFixedBlock.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef FIXED_BLOCK_HH
-#define FIXED_BLOCK_HH
+#ifndef cFixedBlock_h
+#define cFixedBlock_h
/**
* Class used by @ref cBlockStruct.
@@ -16,8 +19,8 @@
private:
int start_point; // Starting point in the cScaledBlock array.
public:
- cFixedBlock();
- ~cFixedBlock();
+ cFixedBlock() : start_point(0) { ; }
+ ~cFixedBlock() { ; }
inline int GetStart() { return start_point; }
inline void SetStart(int in_sp) { start_point = in_sp; }
Modified: development/source/tools/cFixedCoords.h
===================================================================
--- development/source/tools/cFixedCoords.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cFixedCoords.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,14 +1,17 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cFixedCoords.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef FIXED_COORDS_HH
-#define FIXED_COORDS_HH
+#ifndef cFixedCoords_h
+#define cFixedCoords_h
-#ifndef UINT_HH
+#ifndef cUInt_h
#include "cUInt.h"
#endif
@@ -19,8 +22,6 @@
* and offset.
**/
-class cUInt; // aggregate
-
class cFixedCoords {
private:
int block_num;
Modified: development/source/tools/cGenesis.cc
===================================================================
--- development/source/tools/cGenesis.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cGenesis.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,24 +1,18 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cGenesis.cc
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef GENESIS_HH
#include "cGenesis.h"
-#endif
using namespace std;
-/////////////////
-// cGenesis
-/////////////////
-cGenesis::cGenesis()
-{
-}
-
cGenesis::cGenesis(const cString & in_filename) : cInitFile(in_filename)
{
if( !IsOpen() ){
@@ -30,8 +24,6 @@
Close();
}
-//int cGenesis::Open(cString _filename, int mode)
-// porting to gcc 3.1 -- k
int cGenesis::Open(cString _filename, ios::openmode mode)
{
if( IsOpen() ){
Modified: development/source/tools/cGenesis.h
===================================================================
--- development/source/tools/cGenesis.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cGenesis.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,17 +1,20 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cGenesis.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef GENESIS_HH
-#define GENESIS_HH
+#ifndef cGenesis_h
+#define cGenesis_h
-#ifndef INIT_FILE_HH
+#ifndef cInitFile_h
#include "cInitFile.h"
#endif
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
@@ -20,8 +23,6 @@
* the way Avida should run.
*/
-class cString; // aggregate
-
class cGenesis : public cInitFile {
private:
cGenesis(const cGenesis &);
@@ -29,7 +30,7 @@
/**
* The empty constructor creates a clean object.
**/
- cGenesis();
+ cGenesis() { ; }
/**
* This constructor opens the given initialization file, reads it in,
@@ -41,9 +42,6 @@
* Opens an initialization file, reads it in, removes all comments, and
* closes it again.
**/
- //int Open(cString _filename, int mode=(ios::in|ios::nocreate));
- // porting to gcc 3.1
- // nocreate is no longer in the class ios -- k
int Open(cString _filename, std::ios::openmode mode=(std::ios::in));
/**
Modified: development/source/tools/cHelpAlias.cc
===================================================================
--- development/source/tools/cHelpAlias.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cHelpAlias.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,13 +1,18 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cHelpAlias.cc
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
#include "cHelpAlias.h"
+
#include "cHelpFullEntry.h"
+
const cString & cHelpAlias::GetKeyword() const { return full_entry->GetKeyword(); }
const cString & cHelpAlias::GetDesc() const { return full_entry->GetDesc(); }
cHelpType * cHelpAlias::GetType() const { return full_entry->GetType(); }
Modified: development/source/tools/cHelpAlias.h
===================================================================
--- development/source/tools/cHelpAlias.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cHelpAlias.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,14 +1,17 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cHelpAlias.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef HELP_ALIAS_HH
-#define HELP_ALIAS_HH
+#ifndef cHelpAlias_h
+#define cHelpAlias_h
-#ifndef HELP_ENTRY_HH
+#ifndef cHelpEntry_h
#include "cHelpEntry.h"
#endif
Modified: development/source/tools/cHelpEntry.h
===================================================================
--- development/source/tools/cHelpEntry.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cHelpEntry.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,23 +1,24 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cHelpEntry.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef HELP_ENTRY_HH
-#define HELP_ENTRY_HH
+#ifndef cHelpEntry_h
+#define cHelpEntry_h
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
-#ifndef STRING_UTIL_HH
+#ifndef cStringUtil_h
#include "cStringUtil.h"
#endif
class cHelpType;
-class cString; // aggregate
-class cStringUtil; // accessed
class cHelpEntry {
protected:
Modified: development/source/tools/cHelpFullEntry.h
===================================================================
--- development/source/tools/cHelpFullEntry.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cHelpFullEntry.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,26 +1,28 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cHelpFullEntry.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef HELP_FULL_ENTRY_HH
-#define HELP_FULL_ENTRY_HH
+#ifndef cHelpFullEntry_h
+#define cHelpFullEntry_h
-#ifndef HELP_ENTRY_HH
+#ifndef cHelpEntry_h
#include "cHelpEntry.h"
#endif
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
class cHelpType;
-class cString; // aggregate
class cHelpFullEntry : public cHelpEntry {
private:
- cHelpType * type;
+ cHelpType* type;
cString desc;
public:
cHelpFullEntry(const cString & _name, cHelpType * _type, const cString _desc)
@@ -37,7 +39,7 @@
const cString & GetKeyword() const { return name; }
const cString & GetDesc() const { return desc; }
- cHelpType * GetType() const { return type; }
+ cHelpType* GetType() const { return type; }
bool IsAlias() const { return false; }
};
Modified: development/source/tools/cHelpManager.cc
===================================================================
--- development/source/tools/cHelpManager.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cHelpManager.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,32 +1,26 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cHelpManager.cc
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef HELP_MANAGER_HH
#include "cHelpManager.h"
-#endif
-#ifndef HELP_TYPE_HH
#include "cHelpType.h"
-#endif
-#ifndef INIT_FILE_HH
#include "cInitFile.h"
-#endif
-#ifndef STRING_HH
#include "cString.h"
-#endif
-#ifndef TLIST_HH
#include "tList.h"
-#endif
#include <iostream>
using namespace std;
-cHelpType * cHelpManager::GetType(const cString type_name)
+
+cHelpType* cHelpManager::GetType(const cString type_name)
{
// See if we can find this type in the already existant list...
tListIterator<cHelpType> type_it(type_list);
Modified: development/source/tools/cHelpManager.h
===================================================================
--- development/source/tools/cHelpManager.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cHelpManager.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,37 +1,36 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cHelpManager.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef HELP_MANAGER_HH
-#define HELP_MANAGER_HH
+#ifndef cHelpManager_h
+#define cHelpManager_h
-#ifndef HELP_TYPE_HH
+#ifndef cHelpType_h
#include "cHelpType.h"
#endif
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
-#ifndef TLIST_HH
+#ifndef tList_h
#include "tList.h"
#endif
class cHelpFullEntry;
-class cHelpType; // accessed
-class cString; // aggregate
-template <class T> class tList; // aggregate
-template <class T> class tListIterator; // aggregate
class cHelpManager {
private:
tList<cHelpType> type_list;
- cHelpFullEntry * last_entry;
+ cHelpFullEntry* last_entry;
bool verbose; // Should we print messages to the screen?
// Private methods...
- cHelpType * GetType(const cString type_name);
+ cHelpType* GetType(const cString type_name);
private:
// disabled copy constructor.
cHelpManager(const cHelpManager &);
@@ -46,7 +45,7 @@
tListIterator<cHelpType> type_it(type_list);
while (type_it.Next() != NULL) {
- cHelpEntry * found_entry = type_it.Get()->FindEntry(entry_name);
+ cHelpEntry* found_entry = type_it.Get()->FindEntry(entry_name);
if (found_entry != NULL) return found_entry;
}
return NULL;
Modified: development/source/tools/cHelpType.cc
===================================================================
--- development/source/tools/cHelpType.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cHelpType.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,31 +1,25 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cHelpType.cc
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef HELP_TYPE_HH
#include "cHelpType.h"
-#endif
-#ifndef HELP_ALIAS_HH
#include "cHelpAlias.h"
-#endif
-#ifndef HELP_ENTRY_HH
#include "cHelpEntry.h"
-#endif
-#ifndef HELP_FULL_ENTRY_HH
#include "cHelpFullEntry.h"
-#endif
-#ifndef HELP_MANAGER_HH
#include "cHelpManager.h"
-#endif
#include <fstream>
using namespace std;
+
cHelpAlias * cHelpType::AddAlias(const cString & alias_name, cHelpFullEntry * entry) {
cHelpAlias * new_alias = new cHelpAlias(alias_name, entry);
entry_list.Push(new_alias);
Modified: development/source/tools/cHelpType.h
===================================================================
--- development/source/tools/cHelpType.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cHelpType.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,17 +1,20 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cHelpType.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef HELP_TYPE_HH
-#define HELP_TYPE_HH
+#ifndef cHelpType_h
+#define cHelpType_h
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
-#ifndef TLIST_HH
+#ifndef tList_h
#include "tList.h"
#endif
@@ -19,14 +22,12 @@
class cHelpEntry;
class cHelpFullEntry;
class cHelpManager;
-class cString; // aggregate
-template <class T> class tList; // aggregate
class cHelpType {
private:
cString name;
tList<cHelpEntry> entry_list;
- cHelpManager * manager;
+ cHelpManager* manager;
int num_entries;
private:
// disabled copy constructor.
Modified: development/source/tools/cHistogram.cc
===================================================================
--- development/source/tools/cHistogram.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cHistogram.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,17 +1,16 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cHistogram.cc
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef HISTOGRAM_HH
#include "cHistogram.h"
-#endif
-#ifndef FUNCTIONS_HH
#include "functions.h"
-#endif
extern "C" {
#include <stdio.h>
@@ -21,9 +20,9 @@
using namespace std;
-// cHistogram /////////////////////////////////////////////////////////////////
-cHistogram::cHistogram(int in_max, int in_min) {
+cHistogram::cHistogram(int in_max, int in_min)
+{
max_bin = in_max;
min_bin = in_min;
entry_count = 0;
Modified: development/source/tools/cHistogram.h
===================================================================
--- development/source/tools/cHistogram.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cHistogram.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,12 +1,15 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cHistogram.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef HISTOGRAM_HH
-#define HISTOGRAM_HH
+#ifndef cHistogram_h
+#define cHistogram_h
#include <iostream>
@@ -14,6 +17,7 @@
#include <math.h>
}
+
class cHistogram {
private:
int * bins;
Modified: development/source/tools/cID.h
===================================================================
--- development/source/tools/cID.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cID.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,13 +1,16 @@
/*
-Copyright (C) 1993 - 2004 California Institute of Technology
+ * cID.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2004 California Institute of Technology
+ *
+ */
-Read the COPYING and README files, or contact 'avida at alife.org',
-before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE.
-*/
+#ifndef cID_h
+#define cID_h
-#ifndef ID_HH
-#define ID_HH
-
/*!
\brief Provides a unique identifier for instances of a class.
@@ -31,7 +34,7 @@
\note XXX : Don't expect any particular order (although there is \e some well-defined order). The ordering might change if
the current use of pointers to cID objects for their identification turns out to not work.
*/
- cID(){}
+ cID() { ; }
bool operator<(const cID &rhs) const { return this < &rhs; }
bool operator>(const cID &rhs) const { return this > &rhs; }
bool operator<=(const cID &rhs) const { return this <= &rhs; }
Modified: development/source/tools/cIndexedBlockStruct.cc
===================================================================
--- development/source/tools/cIndexedBlockStruct.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cIndexedBlockStruct.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,21 +1,19 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cIndexedBlockStruct.cc
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef INDEXED_BLOCK_STRUCT_HH
#include "cIndexedBlockStruct.h"
-#endif
#include <iostream>
using namespace std;
-//////////////////////////
-// cIndexedBlockStruct
-//////////////////////////
cIndexedBlockStruct::cIndexedBlockStruct(int in_num_scaled, int in_num_fixed,
int in_num_ref)
Modified: development/source/tools/cIndexedBlockStruct.h
===================================================================
--- development/source/tools/cIndexedBlockStruct.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cIndexedBlockStruct.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,10 +1,16 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cIndexedBlockStruct.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
+#ifndef cIndexedBlockStruct_h
+#define cIndexedBlockStruct_h
+
// See block_struct_proto.hh for a good description of this structure.
// This file is a variation of the cBlockStruct data structure. It uses
@@ -15,27 +21,19 @@
// initialized with the maximum reference number which will be passed into
// it (so as to create the third array of that size.
-#ifndef INDEXED_BLOCK_STRUCT_HH
-#define INDEXED_BLOCK_STRUCT_HH
-
-#ifndef FIXED_BLOCK_HH
+#ifndef cFixedBlock_h
#include "cFixedBlock.h"
#endif
-#ifndef FIXED_COORDS_HH
+#ifndef cFixedCoords_h
#include "cFixedCoords.h"
#endif
-#ifndef REF_BLOCK_HH
+#ifndef cRefBlock_h
#include "cRefBlock.h"
#endif
-#ifndef UINT_HH
+#ifndef cUInt_h
#include "cUInt.h"
#endif
-class cFixedBlock; // accessed
-class cRefBlock; // accessed
-class cFixedCoords; // aggregate
-class cUInt; // aggregate
-
class cIndexedBlockStruct {
private:
cFixedBlock * fixed_array;
Modified: development/source/tools/cInitFile.cc
===================================================================
--- development/source/tools/cInitFile.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cInitFile.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,39 +1,20 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cInitFile.cc
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef INIT_FILE_HH
#include "cInitFile.h"
-#endif
-#ifndef STRING_ITERATOR_HH
#include "cStringIterator.h"
-#endif
using namespace std;
-////////////////
-// cInitFile
-////////////////
-cInitFile::cInitFile() : filetype("unknown"), active_line(0)
-{
-}
-
-cInitFile::cInitFile(cString in_filename)
- : cFile(in_filename)
- , filetype("unknown")
- , active_line(0)
-{
-}
-
-cInitFile::~cInitFile()
-{
-}
-
void cInitFile::Load()
{
if (!IsOpen()) return; // The file must be opened!
Modified: development/source/tools/cInitFile.h
===================================================================
--- development/source/tools/cInitFile.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cInitFile.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,25 +1,28 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cInitFile.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef INIT_FILE_HH
-#define INIT_FILE_HH
+#ifndef cInitFile_h
+#define cInitFile_h
#include <iostream>
-#ifndef FILE_HH
+#ifndef cFile_h
#include "cFile.h"
#endif
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
-#ifndef STRING_LIST_HH
+#ifndef cStringList_h
#include "cStringList.h"
#endif
-#ifndef TARRAY_HH
+#ifndef tArray_h
#include "tArray.h"
#endif
@@ -27,10 +30,6 @@
* A class to handle initialization files.
**/
-class cString; // aggregate
-class cStringList; // aggregate
-template <class T> class tArray; // aggregate
-
class cInitFile : public cFile {
private:
cInitFile(const cInitFile &);
@@ -52,16 +51,16 @@
* The empty constructor constructs an object that is in a clean
* state. You can set the file to open with @ref cFile::Open() later on.
**/
- cInitFile();
+ cInitFile() : filetype("unknown"), active_line(0) { ; }
/**
* Opens the file with the given name.
*
* @param in_filename Name of the initialization file to open.
**/
- cInitFile(cString in_filename);
+ cInitFile(cString in_filename) : cFile(in_filename), filetype("unknown"), active_line(0) { ; }
- ~cInitFile();
+ ~cInitFile() { ; }
/**
* Loads the file into memory.
Modified: development/source/tools/cIntSum.cc
===================================================================
--- development/source/tools/cIntSum.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cIntSum.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,14 +1,14 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cIntSum.cc
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef INT_SUM_HH
#include "cIntSum.h"
-#endif
-// cIntSum ///////////////////////////////////////////////////////////////////
const double cIntSum::INF_ERR = 0;
Modified: development/source/tools/cIntSum.h
===================================================================
--- development/source/tools/cIntSum.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cIntSum.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,12 +1,15 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cIntSum.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef INT_SUM_HH
-#define INT_SUM_HH
+#ifndef cIntSum_h
+#define cIntSum_h
#include <math.h>
#include <limits.h>
Modified: development/source/tools/cIntegratedSchedule.cc
===================================================================
--- development/source/tools/cIntegratedSchedule.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cIntegratedSchedule.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cIntegratedSchedule.cc
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
#include "cIntegratedSchedule.h"
@@ -13,13 +16,10 @@
#include "cMerit.h"
#include <iostream>
+
using namespace std;
-/////////////////////////
-// cIntegratedSchedule
-/////////////////////////
-
cIntegratedSchedule::cIntegratedSchedule(int _item_count)
: cSchedule(_item_count)
{
Modified: development/source/tools/cIntegratedSchedule.h
===================================================================
--- development/source/tools/cIntegratedSchedule.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cIntegratedSchedule.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,17 +1,20 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cIntegratedSchedule.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef INTEGRATED_SCHEDULE_HH
-#define INTEGRATED_SCHEDULE_HH
+#ifndef cIntegratedSchedule_h
+#define cIntegratedSchedule_h
-#ifndef SCHEDULE_HH
+#ifndef cSchedule_h
#include "cSchedule.h"
#endif
-#ifndef TARRAY_HH
+#ifndef tArray_h
#include "tArray.h"
#endif
@@ -28,7 +31,6 @@
class cIntegratedScheduleNode;
class cMerit;
-template <class T> class tArray; // aggregate
class cIntegratedSchedule : public cSchedule {
private:
Modified: development/source/tools/cIntegratedScheduleNode.cc
===================================================================
--- development/source/tools/cIntegratedScheduleNode.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cIntegratedScheduleNode.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,17 +1,15 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cIntegratedScheduleNode.cc
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef INTEGRATED_SCHEDULE_NODE_HH
#include "cIntegratedScheduleNode.h"
-#endif
-/////////////////////////////
-// cIntegratedScheduleNode
-/////////////////////////////
cIntegratedScheduleNode::cIntegratedScheduleNode(int _item_count, int in_id)
: active_array(_item_count)
Modified: development/source/tools/cIntegratedScheduleNode.h
===================================================================
--- development/source/tools/cIntegratedScheduleNode.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cIntegratedScheduleNode.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,14 +1,17 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cIntegratedScheduleNode.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef INTEGRATED_SCHEDULE_NODE_HH
-#define INTEGRATED_SCHEDULE_NODE_HH
+#ifndef cIntegratedScheduleNode_h
+#define cIntegratedScheduleNode_h
-#ifndef TARRAY_HH
+#ifndef tArray_h
#include "tArray.h"
#endif
@@ -27,8 +30,6 @@
* each item should be included in.
**/
-template <class T> class tArray; // aggregate
-
class cIntegratedScheduleNode {
private:
tArray<int> active_array; // Each cell in this array corressponds to the
Modified: development/source/tools/cMerit.cc
===================================================================
--- development/source/tools/cMerit.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cMerit.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,15 +1,20 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2001 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cMerit.cc
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2001 California Institute of Technology
+ *
+ */
#include "cMerit.h"
using namespace std;
-void cMerit::UpdateValue(double in_value){
+
+void cMerit::UpdateValue(double in_value)
+{
const int max_bits = sizeof(unsigned int)*8;
static double mult[max_bits];
static bool mult_initilalized = false;
Modified: development/source/tools/cMerit.h
===================================================================
--- development/source/tools/cMerit.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cMerit.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,27 +1,26 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cMerit.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef MERIT_HH
-#define MERIT_HH
+#ifndef cMerit_h
+#define cMerit_h
#include <iostream>
#include <math.h>
#include <limits.h>
#include <assert.h>
-#ifndef UINT
-#define UINT unsigned int
-#endif
-
class cMerit {
protected:
int bits;
- UINT base;
- UINT offset;
+ unsigned int base;
+ unsigned int offset;
double value;
void UpdateValue(double in_value);
@@ -30,7 +29,7 @@
cMerit() : bits(0), base(0), offset(0), value(0) {;}
explicit cMerit(const int in_value){ UpdateValue(in_value); }
- explicit cMerit(const UINT in_value){ UpdateValue(in_value); }
+ explicit cMerit(const unsigned int in_value){ UpdateValue(in_value); }
explicit cMerit(const double in_value){ UpdateValue(in_value); }
bool OK() const ;
@@ -51,23 +50,23 @@
int operator==(const cMerit & _m) const { return value == _m.GetDouble(); }
int operator==(const double _m) const { return value == _m; }
- int operator==(const UINT _m) const { return (offset==0 && base==_m); }
+ int operator==(const unsigned int _m) const { return (offset==0 && base==_m); }
int operator!=(const cMerit & _m) const { return value != _m.GetDouble(); }
int operator!=(const double _m) const { return value != _m; }
- int operator!=(const UINT _m) const { return (offset!=0 || base!=_m); }
+ int operator!=(const unsigned int _m) const { return (offset!=0 || base!=_m); }
void Clear() { value = 0; base = 0; offset = 0; bits = 0; }
// @TCC - This function fails for values > UINT_MAX...
- UINT GetUInt() const {
+ unsigned int GetUInt() const {
assert(value < UINT_MAX); // Fails for merit values > UINT_MAX.
- return (UINT) value; }
+ return (unsigned int) value; }
double GetDouble() const { return value; }
- int GetBit(UINT bit_num) const {
- return ( bit_num >= offset && bit_num < (UINT)bits ) ?
+ int GetBit(unsigned int bit_num) const {
+ return ( bit_num >= offset && bit_num < (unsigned int)bits ) ?
( base >> (bit_num-offset) ) & 1 : 0; }
int GetNumBits() const { return bits; }
Modified: development/source/tools/cMessageClass.h
===================================================================
--- development/source/tools/cMessageClass.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cMessageClass.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,30 +1,33 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cMessageClass.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef MESSAGE_CLASS_HH
-#define MESSAGE_CLASS_HH
+#ifndef cMessageClass_h
+#define cMessageClass_h
class cMessageDisplay;
class cMessageType;
-class cMessageClass{
+class cMessageClass {
public:
cMessageClass(
- const char *class_name,
- cMessageDisplay **msg_display,
+ const char* class_name,
+ cMessageDisplay** msg_display,
bool is_fatal,
bool is_prefix,
bool no_prefix
);
public:
- void configure(cMessageType *message_type);
+ void configure(cMessageType* message_type);
public:
- const char *const m_class_name;
- cMessageDisplay **m_msg_display;
+ const char* const m_class_name;
+ cMessageDisplay** m_msg_display;
bool const m_is_fatal;
bool const m_is_prefix;
bool const m_no_prefix;
Modified: development/source/tools/cMessageClosure.h
===================================================================
--- development/source/tools/cMessageClosure.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cMessageClosure.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,35 +1,37 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cMessageClosure.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef MESSAGE_CLOSURE_HH
-#define MESSAGE_CLOSURE_HH
+#ifndef cMessageClosure_h
+#define cMessageClosure_h
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
class cMessageType;
-class cString; // aggregate
class QString;
class cMessageClosure{
private:
- cMessageType &_type;
- const char *_function;
- const char *_file;
+ cMessageType& _type;
+ const char* _function;
+ const char* _file;
int _line;
int _error;
int _op_count;
cString _msg;
public:
cMessageClosure(
- cMessageType &type,
- const char *function_name,
- const char *file_name,
+ cMessageType& type,
+ const char* function_name,
+ const char* file_name,
int line_number
);
~cMessageClosure(void);
Modified: development/source/tools/cMessageDisplay.cc
===================================================================
--- development/source/tools/cMessageDisplay.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cMessageDisplay.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,27 +1,20 @@
+/*
+ * cMessageDisplay.cc
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ *
+ */
-#ifndef _LIMITS_H___
+#include "cMessageDisplay_headers.h"
+
#include <limits.h>
-#endif
-#ifndef _STDIO_H_
#include <stdio.h>
-#endif
-#ifndef _STDARG_H
#include <stdarg.h>
-#endif
-
-#ifndef TRIO_TRIO_H
#include "../third-party/trio/trio.h"
-#endif
-
-#ifndef _CPP_IOSTREAM
#include <iostream>
-#endif
-#ifndef MESSAGE_DISPLAY_HDRS_HH
-#include "cMessageDisplay_headers.h"
-#endif
-
-
using namespace std;
@@ -35,14 +28,15 @@
the output and error messages can be redirected from, say, the console
to a graphical window and back again (if you want).
*/
-static cMessageDisplay *s_info_display;
-static cMessageDisplay *s_debug_display;
-static cMessageDisplay *s_error_display;
-static cMessageDisplay *s_fatal_display;
-static cMessageDisplay *s_noprefix_display;
+static cMessageDisplay* s_info_display;
+static cMessageDisplay* s_debug_display;
+static cMessageDisplay* s_error_display;
+static cMessageDisplay* s_fatal_display;
+static cMessageDisplay* s_noprefix_display;
+
void setInfoDisplay(cMessageDisplay &info){
cout << "<setInfoDisplay>" << endl;
s_info_display = &info;
Modified: development/source/tools/cMessageDisplay.h
===================================================================
--- development/source/tools/cMessageDisplay.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cMessageDisplay.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,12 +1,14 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cMessageDisplay.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ *
+ */
-#ifndef MESSAGE_DISPLAY_HH
-#define MESSAGE_DISPLAY_HH
+#ifndef cMessageDisplay_h
+#define cMessageDisplay_h
/*
cMessageDisplay displays the message "final_msg" to the user/programmer.
Modified: development/source/tools/cMessageDisplay_headers.h
===================================================================
--- development/source/tools/cMessageDisplay_headers.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cMessageDisplay_headers.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,32 +1,36 @@
-#ifndef MESSAGE_DISPLAY_HDRS_HH
-#define MESSAGE_DISPLAY_HDRS_HH
+/*
+ * cMessageDisplay_headers.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ *
+ */
-#ifndef _CPP_IOSTREAM
+#ifndef cMessageDisplay_headers_h
+#define cMessageDisplay_headers_h
+
#include <iostream>
-#endif
-#ifndef DEFAULT_MESSAGE_DISPLAY_HH
+
+#ifndef cDefaultMessageDisplay_h
#include "cDefaultMessageDisplay.h"
#endif
-#ifndef MESSAGE_CLASS_HH
+#ifndef cMessageClass_h
#include "cMessageClass.h"
#endif
-#ifndef MESSAGE_CLOSURE_HH
+#ifndef cMessageClosure_h
#include "cMessageClosure.h"
#endif
-#ifndef MESSAGE_DISPLAY_HH
+#ifndef cMessageDisplay_h
#include "cMessageDisplay.h"
#endif
-#ifndef MESSAGE_TYPE_HH
+#ifndef cMessageType_h
#include "cMessageType.h"
#endif
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
-#ifndef MESSAGE_DISPLAY_HH
-#include "cMessageDisplay.h"
-#endif
-
extern cMessageType NoPrefix_Msg;
extern cMessageType Info_GEN_Msg;
extern cMessageType Debug_GEN_Msg;
Modified: development/source/tools/cMessageType.h
===================================================================
--- development/source/tools/cMessageType.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cMessageType.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,24 +1,27 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cMessageType.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef MESSAGE_TYPE_HH
-#define MESSAGE_TYPE_HH
+#ifndef cMessageType_h
+#define cMessageType_h
class cMessageClass;
class cMessageType{
public:
cMessageType(
- const char *type_name,
- cMessageClass &message_class
+ const char* type_name,
+ cMessageClass& message_class
);
public:
- const char *m_type_name;
- const cMessageClass &m_message_class;
+ const char* m_type_name;
+ const cMessageClass& m_message_class;
bool m_is_active;
};
Modified: development/source/tools/cProbSchedule.cc
===================================================================
--- development/source/tools/cProbSchedule.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cProbSchedule.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cProbSchedule.cc
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
#include "cProbSchedule.h"
@@ -12,10 +15,6 @@
#include "cWorld.h"
-///////////////////
-// cProbSchedule
-///////////////////
-
// The larger merits cause problems here; things need to be re-thought out.
cProbSchedule::cProbSchedule(cWorld* world, int _item_count)
Modified: development/source/tools/cProbSchedule.h
===================================================================
--- development/source/tools/cProbSchedule.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cProbSchedule.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,17 +1,20 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cProbSchedule.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef PROB_SCHEDULE_HH
-#define PROB_SCHEDULE_HH
+#ifndef cProbSchedule_h
+#define cProbSchedule_h
-#ifndef SCHEDULE_HH
+#ifndef cSchedule_h
#include "cSchedule.h"
#endif
-#ifndef WEIGHTED_INDEX_HH
+#ifndef cWeightedIndex_h
#include "cWeightedIndex.h"
#endif
@@ -20,7 +23,6 @@
* be scheduled proportional to the merit of that item.
**/
-class cWeightedIndex; // aggregate
class cMerit;
class cWorld;
Modified: development/source/tools/cRandom.cc
===================================================================
--- development/source/tools/cRandom.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cRandom.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,21 +1,17 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2000 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cRandom.cc
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2000 California Institute of Technology
+ *
+ */
-#ifndef cRandom_h
#include "cRandom.h"
-#endif
-#ifndef TARRAY_HH
#include "tArray.h"
-#endif
-/* FIXME this is not defined in Visual Studio.net. -- kgn */
-//#ifdef MSVC_COMPILER
-/* FIXME find out what the VS.n macro might be. for now use WIN32 -- kgn */
#ifdef WIN32
#include <process.h>
#else
Modified: development/source/tools/cRandom.h
===================================================================
--- development/source/tools/cRandom.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cRandom.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,19 +1,13 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cRandom.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2000 California Institute of Technology
+ *
+ */
-/******************************************************************************
-
-cRandom
-
-Random number generator
-Random variables from various statistical distributions
-
-******************************************************************************/
-
#ifndef cRandom_h
#define cRandom_h
@@ -21,17 +15,13 @@
#include <limits.h>
#include <math.h>
-#ifndef UINT
-#define UINT unsigned int
-#endif
-
/**
* A versatile and fast pseudo random number generator.
**/
template <class T> class tArray;
-class cRandom{
+class cRandom {
public:
/**
* Set up the random generator object.
@@ -138,10 +128,10 @@
// Other neat stuff /////////////////////////////////////////////////////////
- inline UINT MutateByte(UINT value);
- inline UINT ClearByte(UINT value);
- inline UINT MutateBit(UINT value);
- inline UINT MutateBit(UINT value, int in_byte);
+ inline unsigned int MutateByte(unsigned int value);
+ inline unsigned int ClearByte(unsigned int value);
+ inline unsigned int MutateBit(unsigned int value);
+ inline unsigned int MutateBit(unsigned int value, int in_byte);
bool Choose(int num_in, tArray<int> & out_array);
@@ -241,7 +231,7 @@
};
-inline UINT cRandom::MutateByte(UINT value) {
+inline unsigned int cRandom::MutateByte(unsigned int value) {
int byte_pos = 8 * GetUInt(4);
int new_byte = GetUInt(256);
value &= ~(255 << byte_pos);
@@ -249,19 +239,19 @@
return value;
}
-inline UINT cRandom::ClearByte(UINT value) {
+inline unsigned int cRandom::ClearByte(unsigned int value) {
int byte_pos = 8 * GetUInt(4);
value &= ~(255 << byte_pos);
return value;
}
-inline UINT cRandom::MutateBit(UINT value) {
+inline unsigned int cRandom::MutateBit(unsigned int value) {
int bit_pos = GetUInt(32);
value ^= (1 << bit_pos);
return value;
}
-inline UINT cRandom::MutateBit(UINT value, int in_byte) {
+inline unsigned int cRandom::MutateBit(unsigned int value, int in_byte) {
int bit_pos = (in_byte) * 8 + GetUInt(8);
value ^= (1 << bit_pos);
return value;
Deleted: development/source/tools/cRefBlock.cc
===================================================================
--- development/source/tools/cRefBlock.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cRefBlock.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,25 +0,0 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
-
-#ifndef REF_BLOCK_HH
-#include "cRefBlock.h"
-#endif
-
-////////////////////
-// cRefBlock
-////////////////////
-
-cRefBlock::cRefBlock(int in_ref, int in_size)
-{
- ref_num = in_ref;
- size = in_size;
-}
-
-cRefBlock::~cRefBlock()
-{
- // nothing needed here...
-}
Modified: development/source/tools/cRefBlock.h
===================================================================
--- development/source/tools/cRefBlock.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cRefBlock.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,27 +1,28 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cRefBlock.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef REF_BLOCK_HH
-#define REF_BLOCK_HH
+#ifndef cRefBlock_h
+#define cRefBlock_h
-#ifndef FIXED_COORDS_HH
+#ifndef cFixedCoords_h
#include "cFixedCoords.h"
#endif
-class cFixedCoords; // aggregate
-
class cRefBlock {
private:
int ref_num;
int size;
cFixedCoords start_coords;
public:
- cRefBlock(int in_ref = 0, int in_size = 0);
- ~cRefBlock();
+ cRefBlock(int in_ref = 0, int in_size = 0) ref_num(in_ref), size(in_size) { ; }
+ ~cRefBlock() { ; }
inline int GetRef() const { return ref_num; }
inline int GetSize() const { return size; }
Modified: development/source/tools/cRunningAverage.cc
===================================================================
--- development/source/tools/cRunningAverage.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cRunningAverage.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,17 +1,17 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cRunningAverage.cc
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef RUNNING_AVERAGE_HH
#include "cRunningAverage.h"
-#endif
#include <assert.h>
-// cRunningAverage ////////////////////////////////////////////////////////////
cRunningAverage::cRunningAverage( int window_size ) :
m_values(0), m_s1(0), m_s2(0), m_window_size( window_size ),
@@ -27,15 +27,13 @@
}
-void
-cRunningAverage::Add( double value ) {
+void cRunningAverage::Add( double value ) {
m_s1 += value;
m_s2 += value*value;
if ( m_n < m_window_size ) {
m_values[ m_n ] = value;
m_n += 1;
- }
- else{
+ } else {
double out_v = m_values[ m_pointer ];
m_s1 -= out_v;
m_s2 -= out_v * out_v;
@@ -45,8 +43,7 @@
}
-void
-cRunningAverage::Clear() {
+void cRunningAverage::Clear() {
m_s1 = 0;
m_s2 = 0;
m_pointer = 0;
Modified: development/source/tools/cRunningAverage.h
===================================================================
--- development/source/tools/cRunningAverage.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cRunningAverage.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,12 +1,15 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cRunningAverage.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef RUNNING_AVERAGE_HH
-#define RUNNING_AVERAGE_HH
+#ifndef cRunningAverage_h
+#define cRunningAverage_h
#include <math.h>
Deleted: development/source/tools/cScaledBlock.cc
===================================================================
--- development/source/tools/cScaledBlock.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cScaledBlock.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,26 +0,0 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2000 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
-
-#ifndef SCALED_BLOCK_HH
-#include "cScaledBlock.h"
-#endif
-
-////////////////////
-// cScaledBlock
-////////////////////
-
-cScaledBlock::cScaledBlock(void * in_data, int in_size)
-{
- data = in_data;
- size = in_size;
-}
-
-cScaledBlock::~cScaledBlock()
-{
-}
-
-
Modified: development/source/tools/cScaledBlock.h
===================================================================
--- development/source/tools/cScaledBlock.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cScaledBlock.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,14 +1,17 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cScaledBlock.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef SCALED_BLOCK_HH
-#define SCALED_BLOCK_HH
+#ifndef cScaledBlock_h
+#define cScaledBlock_h
-#ifndef FIXED_COORDS_HH
+#ifndef cFixedCoords_h
#include "cFixedCoords.h"
#endif
@@ -16,16 +19,14 @@
* Class used by @ref cBlockStruct.
**/
-class cFixedCoords; // aggregate
-
class cScaledBlock {
private:
void * data;
int size;
cFixedCoords start_coords;
public:
- cScaledBlock(void * in_data = NULL, int in_size = 0);
- ~cScaledBlock();
+ cScaledBlock(void * in_data = NULL, int in_size = 0) : data(in_data), size(in_size) { ; }
+ ~cScaledBlock() { ; }
inline void * GetData() const { return data; }
inline int GetSize() const { return size; }
Modified: development/source/tools/cSchedule.cc
===================================================================
--- development/source/tools/cSchedule.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cSchedule.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,17 +1,17 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cSchedule.cc
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
#include "cSchedule.h"
#include "cChangeList.h"
-////////////////
-// cSchedule
-////////////////
cSchedule::cSchedule(int _item_count)
: item_count(_item_count)
Modified: development/source/tools/cSchedule.h
===================================================================
--- development/source/tools/cSchedule.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cSchedule.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,12 +1,15 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cSchedule.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef SCHEDULE_HH
-#define SCHEDULE_HH
+#ifndef cSchedule_h
+#define cSchedule_h
/**
* This class is the base object to handle time-slicing. All other schedulers
@@ -16,10 +19,11 @@
class cMerit;
class cChangeList;
+
class cSchedule {
protected:
int item_count;
- cChangeList *m_change_list;
+ cChangeList* m_change_list;
public:
cSchedule(int _item_count);
virtual ~cSchedule();
Modified: development/source/tools/cString.cc
===================================================================
--- development/source/tools/cString.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cString.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,9 +1,12 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cString.cc
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
#include "cString.h"
Modified: development/source/tools/cString.h
===================================================================
--- development/source/tools/cString.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cString.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,12 +1,15 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cString.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef STRING_HH
-#define STRING_HH
+#ifndef cString_h
+#define cString_h
#include <stdlib.h>
#include <iostream>
Modified: development/source/tools/cStringIterator.cc
===================================================================
--- development/source/tools/cStringIterator.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cStringIterator.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,21 +1,19 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cStringIterator.cc
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef STRING_ITERATOR_HH
#include "cStringIterator.h"
-#endif
-#ifndef STRING_HH
#include "cString.h"
-#endif
-#ifndef STRING_LIST_HH
#include "cStringList.h"
-#endif
+
const cString cStringIterator::null_str("");
cStringIterator::cStringIterator(const cStringList & in_list)
Modified: development/source/tools/cStringIterator.h
===================================================================
--- development/source/tools/cStringIterator.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cStringIterator.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,24 +1,26 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cStringIterator.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef STRING_ITERATOR_HH
-#define STRING_ITERATOR_HH
+#ifndef cStringIterator_h
+#define cStringIterator_h
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
-#ifndef TLIST_HH
+#ifndef tList_h
#include "tList.h"
#endif
-class cString; // aggregate
class cStringList;
-template <class T> class tConstListIterator; // aggregate
+
class cStringIterator {
private:
tConstListIterator<cString> list_it;
Modified: development/source/tools/cStringList.cc
===================================================================
--- development/source/tools/cStringList.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cStringList.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,23 +1,21 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cStringList.cc
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
+#include "cStringList.h"
+
#include "functions.h"
-#ifndef STRING_ITERATOR_HH
#include "cStringIterator.h"
-#endif
-#ifndef STRING_LIST_HH
-#include "cStringList.h"
-#endif
-
using namespace std;
-
cStringList::cStringList(const cString & _list, char seperator)
{
Load(_list, seperator);
Modified: development/source/tools/cStringList.h
===================================================================
--- development/source/tools/cStringList.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cStringList.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,22 +1,23 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cStringList.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef STRING_LIST_HH
-#define STRING_LIST_HH
+#ifndef cStringList_h
+#define cStringList_h
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
-#ifndef TLIST_HH
+#ifndef tList_h
#include "tList.h"
#endif
-class cString; // aggregate
-template <class T> class tList; // aggregate
class cStringList {
private:
Modified: development/source/tools/cStringUtil.cc
===================================================================
--- development/source/tools/cStringUtil.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cStringUtil.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,15 +1,15 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2001 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cStringUtil.cc
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef STRING_UTIL_HH
#include "cStringUtil.h"
-#endif
-
#include "functions.h"
#include "tMatrix.h"
@@ -18,7 +18,6 @@
#include <stdarg.h>
}
-
using namespace std;
Modified: development/source/tools/cStringUtil.h
===================================================================
--- development/source/tools/cStringUtil.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cStringUtil.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,19 +1,20 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cStringUtil.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef STRING_UTIL_HH
-#define STRING_UTIL_HH
+#ifndef cStringUtil_h
+#define cStringUtil_h
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
-class cString; // aggregate
-
struct cStringUtil {
static cString Stringf(const char * fmt, ...);
static cString ToRomanNumeral(const int in_value);
Modified: development/source/tools/cTools.cc
===================================================================
--- development/source/tools/cTools.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cTools.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,22 +1,21 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2001 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cTools.cc
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2001 California Institute of Technology
+ *
+ */
-#ifndef TOOLS_HH
#include "cTools.h"
-#endif
#include <iostream>
#include <errno.h>
#include <sys/stat.h>
#include <stdio.h>
-#ifndef STRING_HH
#include "cString.h"
-#endif
#ifdef WIN32
# ifndef WIN32_MKDIR_HACK_HH
@@ -26,6 +25,7 @@
using namespace std;
+
bool cTools::MkDir(const cString & dirname, bool verbose)
{
if (verbose) cout << "Checking for directory '" << dirname << "'..." << flush;
Modified: development/source/tools/cTools.h
===================================================================
--- development/source/tools/cTools.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cTools.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,15 +1,16 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cTools.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-// This file is for misc. objects which are of general use...
+#ifndef cTools_h
+#define cTools_h
-#ifndef TOOLS_HH
-#define TOOLS_HH
-
/*
* Filesystem tools...
*/
@@ -18,7 +19,7 @@
class cTools {
public:
- static bool MkDir(const cString & dirname, bool verbose=false);
+ static bool MkDir(const cString& dirname, bool verbose=false);
};
#endif
Modified: development/source/tools/cUInt.h
===================================================================
--- development/source/tools/cUInt.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cUInt.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,19 +1,18 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cUInt.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef UINT_HH
-#define UINT_HH
+#ifndef cUInt_h
+#define cUInt_h
#include <stdio.h>
-#ifndef UCHAR
-#define UCHAR unsigned char
-#endif
-
// Should this just use a long? For testing only...
#define LONG_C_UINT
@@ -35,7 +34,7 @@
inline void ShiftLeft(int num_bytes = 1) { value = value << (8 * num_bytes);}
inline void ShiftRight(int num_bytes = 1){ value = value >> (8 * num_bytes);}
- inline cUInt& operator=(const UCHAR in_char) {
+ inline cUInt& operator=(const unsigned char in_char) {
value = (long) in_char;
return *this;
}
@@ -48,7 +47,7 @@
return *this;
}
- inline cUInt& operator*=(const UCHAR in_char){
+ inline cUInt& operator*=(const unsigned char in_char){
value *= (long) in_char;
return *this;
}
@@ -188,10 +187,9 @@
}
};
-#endif
-#ifndef LONG_C_UINT
+#else /* LONG_C_UINT */
/**
* This class constructs an arbitrary (pre-set) large integer. Not all of the
@@ -200,7 +198,7 @@
class cUInt {
private:
- UCHAR * value;
+ unsigned char * value;
int size;
public:
@@ -217,17 +215,17 @@
inline int GetSize() const { return size; }
inline int GetSizeUsed() const;
- inline UCHAR GetByte(int byte_num) const { return value[byte_num]; }
- inline void SetByte(int byte_num, UCHAR in_char) {value[byte_num] = in_char;}
+ inline unsigned char GetByte(int byte_num) const { return value[byte_num]; }
+ inline void SetByte(int byte_num, unsigned char in_char) {value[byte_num] = in_char;}
inline void ShiftLeft(int num_bytes = 1);
inline void ShiftRight(int num_bytes = 1);
- inline cUInt& operator=(const UCHAR in_char);
+ inline cUInt& operator=(const unsigned char in_char);
inline cUInt& operator=(const int in_int);
inline cUInt& operator=(const cUInt& in_cUInt);
- inline cUInt& operator*=(const UCHAR in_char);
+ inline cUInt& operator*=(const unsigned char in_char);
inline cUInt& operator+=(const int in_int);
inline cUInt& operator-=(const int in_int);
@@ -314,7 +312,7 @@
{
int i;
size = 10;
- value = new UCHAR[size];
+ value = new unsigned char[size];
for (i = 0; i < size; i++) {
value[i] = 0;
}
@@ -325,7 +323,7 @@
int i;
size = in_size;
- value = new UCHAR[size];
+ value = new unsigned char[size];
for (i = 0; i < size; i++) {
value[i] = 0;
}
@@ -336,9 +334,9 @@
int i;
size = in_size;
- value = new UCHAR[size];
+ value = new unsigned char[size];
for (i = 0; i < size && i < 4; i++) {
- value[i] = (UCHAR) (in_value >> (8 * i));
+ value[i] = (unsigned char) (in_value >> (8 * i));
}
while (i < size) {
value[i++] = 0;
@@ -352,7 +350,7 @@
inline void cUInt::Resize(int new_size)
{
- UCHAR * new_value = new UCHAR[new_size];
+ unsigned char * new_value = new unsigned char[new_size];
int i;
for (i = 0; i < new_size && i < size; i++) {
@@ -462,7 +460,7 @@
}
}
-inline cUInt& cUInt::operator=(const UCHAR in_char)
+inline cUInt& cUInt::operator=(const unsigned char in_char)
{
int i;
value[0] = in_char;
@@ -477,7 +475,7 @@
{
int i;
for (i = 0; i < 4 && i < size; i++) {
- value[i] = (UCHAR) (in_int >> (8*i));
+ value[i] = (unsigned char) (in_int >> (8*i));
}
for (i = 4; i < size; i++) {
value[i] = 0;
@@ -501,7 +499,7 @@
return *this;
}
-inline cUInt& cUInt::operator*=(const UCHAR in_char)
+inline cUInt& cUInt::operator*=(const unsigned char in_char)
{
int this_byte = 0, carry = 0;
int i;
@@ -565,14 +563,14 @@
for (i = 0; i < size && i < in_cUInt.GetSize(); i++) {
cur_sum += value[i];
cur_sum += in_cUInt.GetByte(i);
- value[i] = (UCHAR) (cur_sum & 255);
+ value[i] = (unsigned char) (cur_sum & 255);
cur_sum = cur_sum >> 8;
}
// If there is still a remainder, and room for it, continue.
while (cur_sum && i < size) {
- value[i++] = (UCHAR) (cur_sum & 255);
+ value[i++] = (unsigned char) (cur_sum & 255);
}
return *this;
@@ -587,11 +585,11 @@
byte1 = (int) value[i];
byte2 = (int) in_cUInt.GetByte(i);
if (byte1 + next_byte >= byte2) {
- value[i] = (UCHAR) (byte1 + next_byte - byte2);
+ value[i] = (unsigned char) (byte1 + next_byte - byte2);
next_byte = 0;
}
else {
- value[i] = (UCHAR) (256 + byte1 + next_byte - byte2);
+ value[i] = (unsigned char) (256 + byte1 + next_byte - byte2);
next_byte = -1;
}
}
@@ -604,7 +602,7 @@
next_byte = 0;
}
else {
- value[i] = (UCHAR) (256 + next_byte + (int) value[i]);
+ value[i] = (unsigned char) (256 + next_byte + (int) value[i]);
next_byte = -1;
}
}
Modified: development/source/tools/cVerifierSuiteRecurser.h
===================================================================
--- development/source/tools/cVerifierSuiteRecurser.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cVerifierSuiteRecurser.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,14 +1,17 @@
/*
-Copyright (C) 1993 - 2004 California Institute of Technology
+ * cVerifierSuiteRecurser.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2004 California Institute of Technology
+ *
+ */
-Read the COPYING and README files, or contact 'avida at alife.org',
-before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE.
-*/
+#ifndef cVerifierSuiteRecurser_h
+#define cVerifierSuiteRecurser_h
-#ifndef VERIFIER_SUITE_RECURSER_HH
-#define VERIFIER_SUITE_RECURSER_HH
-
-#ifndef CYCLE_CHECK_HH
+#ifndef cCycleCheck_h
#include "cCycleCheck.h"
#endif
Modified: development/source/tools/cWeightedIndex.cc
===================================================================
--- development/source/tools/cWeightedIndex.cc 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cWeightedIndex.cc 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,16 +1,17 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2002 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cWeighedIndex.cc
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef WEIGHTED_INDEX_HH
#include "cWeightedIndex.h"
-#endif
+
#include <iostream>
-
using namespace std;
Modified: development/source/tools/cWeightedIndex.h
===================================================================
--- development/source/tools/cWeightedIndex.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/cWeightedIndex.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,14 +1,17 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * cWeightedIndex.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef WEIGHTED_INDEX_HH
-#define WEIGHTED_INDEX_HH
+#ifndef cWeightedIndex_h
+#define cWeightedIndex_h
-#ifndef TARRAY_HH
+#ifndef tArray_h
#include "tArray.h"
#endif
@@ -21,8 +24,6 @@
* that weight.
**/
-template <class T> class tArray; // aggregate
-
class cWeightedIndex {
protected:
int size;
Modified: development/source/tools/functions.h
===================================================================
--- development/source/tools/functions.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/functions.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,24 +1,25 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * functions.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef FUNCTIONS_HH
-#define FUNCTIONS_HH
+#ifndef functions_h
+#define functions_h
#include <iostream>
#include <math.h>
#include <stdio.h>
#include <assert.h>
-#ifndef TARRAY_HH
+#ifndef tArray_h
#include "tArray.h"
#endif
-template <class T> class tArray; // accessed
-
#ifndef NULL
#define NULL 0
#endif
@@ -30,10 +31,7 @@
inline int Pow(int bas, int expon);
inline double Log(double value);
-//////////////////////
-// Generic (inline) functions...
-//////////////////////
-
+
namespace nFunctions {
inline void Swap(int & in1, int & in2)
Modified: development/source/tools/tArgDataEntry.h
===================================================================
--- development/source/tools/tArgDataEntry.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/tArgDataEntry.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,17 +1,19 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * tArgDataEntry.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
+#ifndef tArgDataEntry_h
+#define tArgDataEntry_h
-#ifndef TARGDATAENTRY_HH
-#define TARGDATAENTRY_HH
-
#include <iostream>
-#ifndef TDATAENTRYBASE_HH
+#ifndef tDataEntryBase_h
#include "tDataEntryBase.h"
#endif
Modified: development/source/tools/tArray.h
===================================================================
--- development/source/tools/tArray.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/tArray.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,12 +1,17 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * tArray.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
+#ifndef tArray_h
+#define tArray_h
+
/*
- tArray.h
Array Templates
Constructor:
@@ -29,9 +34,6 @@
return the element at index in the array
*/
-#ifndef TARRAY_HH
-#define TARRAY_HH
-
#include <assert.h>
#ifndef NULL
@@ -156,4 +158,4 @@
};
-#endif // TARRAY_HH
+#endif
Modified: development/source/tools/tBuffer.h
===================================================================
--- development/source/tools/tBuffer.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/tBuffer.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,26 +1,26 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * tBuffer.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef TBUFFER_HH
-#define TBUFFER_HH
+#ifndef tBuffer_h
+#define tBuffer_h
#include <assert.h>
#include <iostream>
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
-#ifndef TARRAY_HH
+#ifndef tArray_h
#include "tArray.h"
#endif
-template <class T> class tArray; // aggregate
-class cString; // aggregate
-
template <class T> class tBuffer {
private:
tArray<T> data; // Contents of buffer...
Modified: development/source/tools/tDataEntry.h
===================================================================
--- development/source/tools/tDataEntry.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/tDataEntry.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,28 +1,28 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * tDataEntry.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef TDATAENTRY_HH
-#define TDATAENTRY_HH
+#ifndef tDataEntry_h
+#define tDataEntry_h
#include <iostream>
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
-#ifndef STRING_UTIL_HH
+#ifndef cStringUtil_h
#include "cStringUtil.h"
#endif
-#ifndef TDATAENTRYBASE_HH
+#ifndef tDataEntryBase_h
#include "tDataEntryBase.h"
#endif
-class cString;
-struct cStringUtil; // access
-
template <class T, class OUT> class tDataEntry : public tDataEntryBase<T> {
protected:
OUT (T::*DataRetrieval)() const;
Modified: development/source/tools/tDataEntryBase.h
===================================================================
--- development/source/tools/tDataEntryBase.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/tDataEntryBase.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,22 +1,23 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * tDataEntryBase.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef TDATAENTRYBASE_HH
-#define TDATAENTRYBASE_HH
+#ifndef tDataEntryBase_h
+#define tDataEntryBase_h
#include <iostream>
#include <sstream>
-#ifndef DATA_ENTRY_HH
+#ifndef cDataEntry_h
#include "cDataEntry.h"
#endif
-using namespace std;
-
class cString;
template <class T> class tDataEntryBase : public cDataEntry {
@@ -57,7 +58,7 @@
}
cString AsString() {
- stringstream tmp_stream;
+ std::stringstream tmp_stream;
tmp_stream << *this;
cString out_str;
tmp_stream >> out_str;
Modified: development/source/tools/tDataEntryCommand.h
===================================================================
--- development/source/tools/tDataEntryCommand.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/tDataEntryCommand.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,26 +1,28 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * tDataEntryCommand.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef TDATAENTRYCOMMAND_HH
-#define TDATAENTRYCOMMAND_HH
+#ifndef tDataEntryCommand_h
+#define tDataEntryCommand_h
#include <iostream>
-#ifndef STRING_LIST_HH
+#ifndef cStringList_h
#include "cStringList.h"
#endif
-#ifndef TDATAENTRYBASE_HH
+#ifndef tDataEntryBase_h
#include "tDataEntryBase.h"
#endif
class cString;
-class cStringList; // aggregate
-template <class T> class tDataEntryBase; // access
+
template <class T> class tDataEntryCommand {
private:
tDataEntryBase<T> * data_entry;
Modified: development/source/tools/tDataManager.h
===================================================================
--- development/source/tools/tDataManager.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/tDataManager.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,22 +1,25 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * tDataManager.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef TDATAMANAGER_HH
-#define TDATAMANAGER_HH
+#ifndef tDataManager_h
+#define tDataManager_h
#include <iostream>
-#ifndef DATA_MANAGER_BASE_HH
+#ifndef cDataManager_Base_h
#include "cDataManager_Base.h"
#endif
-#ifndef TDATAENTRYBASE_HH
+#ifndef tDataEntryBase_h
#include "tDataEntryBase.h"
#endif
-#ifndef TDICTIONARY_HH
+#ifndef tDictionary_h
#include "tDictionary.h"
#endif
@@ -27,8 +30,6 @@
class cString;
template <class T, class U> class tDataEntry;
-template <class T> class tDataEntryBase; // access
-template <class T> class tDictionary; // aggregate
template <class T> class tDataManager : public cDataManager_Base {
private:
Modified: development/source/tools/tDictionary.h
===================================================================
--- development/source/tools/tDictionary.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/tDictionary.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -5,7 +5,12 @@
* Created by David on 10/11/05.
* Copyright 2005 Michigan State University. All rights reserved.
*
- *
+ */
+
+#ifndef tDictionary_h
+#define tDictionary_h
+
+/*
* This template is used to look up objects of the desired type by name.
* It is essentially a wrapper around tHashTable<cString, DATA_TYPE>, with
* the addition of NearMatch().
@@ -13,16 +18,13 @@
* For details about the encapsulated methods, see tHashTable.
*/
-#ifndef TDICTIONARY_HH
-#define TDICTIONARY_HH
-
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
-#ifndef STRING_UTIL_HH
+#ifndef cStringUtil_h
#include "cStringUtil.h"
#endif
-#ifndef THASH_TABLE_HH
+#ifndef tHashTable_h
#include "tHashTable.h"
#endif
Modified: development/source/tools/tHashTable.h
===================================================================
--- development/source/tools/tHashTable.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/tHashTable.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,10 +1,16 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2005 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * tHashTable.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
+#ifndef tHashTable_h
+#define tHashTable_h
+
/*
* This template is used to look up objects of the desired type by an integer
* hash ID. It is implemented through use of a linked list that contains all
@@ -44,16 +50,13 @@
* the lookup finds an entry not in the current cell (lookup fails).
*/
-#ifndef THASH_TABLE_HH
-#define THASH_TABLE_HH
-
-#ifndef STRING_HH
+#ifndef cString_h
#include "cString.h"
#endif
-#ifndef TARRAY_HH
+#ifndef tArray_h
#include "tArray.h"
#endif
-#ifndef TLIST_HH
+#ifndef tList_h
#include "tList.h"
#endif
Modified: development/source/tools/tList.h
===================================================================
--- development/source/tools/tList.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/tList.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,12 +1,15 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * tList.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef TLIST_HH
-#define TLIST_HH
+#ifndef tList_h
+#define tList_h
#ifndef NULL
#define NULL 0
Modified: development/source/tools/tMatrix.h
===================================================================
--- development/source/tools/tMatrix.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/tMatrix.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,12 +1,17 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * tMatrix.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
+#ifndef tMatrix_h
+#define tMatrix_h
+
/*
- tMatrix.h
Matrix Templates
Constructor:
@@ -33,12 +38,9 @@
*/
-#ifndef TMATRIX_HH
-#define TMATRIX_HH
-
#include <assert.h>
-#ifndef TARRAY_HH
+#ifndef tArray_h
#include "tArray.h"
#endif
@@ -46,8 +48,6 @@
* This class provides a matrix template.
**/
-template <class T> class tArray; // access
-
template <class T> class tMatrix {
protected:
// Internal Variables
@@ -140,4 +140,4 @@
virtual ~tMatrix(){ if(data!=NULL) delete [] data; }
};
-#endif // TARRAY_HH
+#endif
Modified: development/source/tools/tMemTrack.h
===================================================================
--- development/source/tools/tMemTrack.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/tMemTrack.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,12 +1,15 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * tMemTrack.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef TMEM_TRACK_HH
-#define TMEM_TRACK_HH
+#ifndef tMemTrack_h
+#define tMemTrack_h
template <class T> class tMemTrack {
private:
Modified: development/source/tools/tObjectFactory.h
===================================================================
--- development/source/tools/tObjectFactory.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/tObjectFactory.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -7,16 +7,16 @@
*
*/
-#ifndef TOBJECTFACTORY_H
-#define TOBJECTFACTORY_H
+#ifndef tObjectFactory_h
+#define tObjectFactory_h
-#ifndef TDICTIONARY_HH
+#ifndef tDictionary_h
#include "tDictionary.h"
#endif
-#ifndef TARRAY_HH
+#ifndef tArray_h
#include "tArray.h"
#endif
-#ifndef TLIST_HH
+#ifndef tList_h
#include "tList.h"
#endif
Modified: development/source/tools/tVector.h
===================================================================
--- development/source/tools/tVector.h 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/tVector.h 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,12 +1,15 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
+/*
+ * tVector.h
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-#ifndef TVECTOR_HH
-#define TVECTOR_HH
+#ifndef tVector_h
+#define tVector_h
/**
* This class provides a vector template.
Modified: development/source/tools/tVerifierSuite.hh
===================================================================
--- development/source/tools/tVerifierSuite.hh 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/tVerifierSuite.hh 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,15 +1,18 @@
/*
-Copyright (C) 1993 - 2004 California Institute of Technology
+ * tVerifierSuite.hh
+ * Avida
+ *
+ * Created by David on 12/7/05.
+ * Copyright 2005 Michigan State University. All rights reserved.
+ * Copyright 1993-2003 California Institute of Technology
+ *
+ */
-Read the COPYING and README files, or contact 'avida at alife.org',
-before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE.
-*/
-
-#ifndef T_VERIFIER_SUITE_HH
-#define T_VERIFIER_SUITE_HH
+#ifndef tVerifierSuite_hh
+#define tVerifierSuite_hh
#endif
-#ifndef VERIFIER_SUITE_RECURSER_HH
+#ifndef cVerifierSuiteRecurser_h
#include "cVerifierSuiteRecurser.h"
#endif
Modified: development/source/tools/win32_mkdir_hack.hh
===================================================================
--- development/source/tools/win32_mkdir_hack.hh 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/tools/win32_mkdir_hack.hh 2005-12-07 23:44:39 UTC (rev 414)
@@ -15,7 +15,7 @@
# define mkdir(path, ignored_mode) _mkdir(path)
# endif
# ifndef mode_t
-# define mode_t UINT
+# define mode_t unsigned int
# endif
#endif
Deleted: development/source/utils/fixHeaders.py
===================================================================
--- development/source/utils/fixHeaders.py 2005-12-07 21:01:20 UTC (rev 413)
+++ development/source/utils/fixHeaders.py 2005-12-07 23:44:39 UTC (rev 414)
@@ -1,65 +0,0 @@
-#!/usr/bin/env python
-#
-# Fix the copyright lines in the file headers
-
-import re, os
-
-# Precompile some regexes
-dateRE = re.compile( r"(^//.*Copyright.*)(\d.*\d)(.*California.*Technology.*$)" );
-licRE = re.compile( r"(^//.*)((?:LICENSE)|(?:COPYING))(.*)('.*',)(.*$)" );
-sourceRE = re.compile( \
- r"(\.cc\b)|(\.hh\b)|(\.ii\b)|(\.c\b)|(\.h\b)|(\.java\b)" )
-
-# The canonical copyright
-cprString = [\
-"//////////////////////////////////////////////////////////////////////////////\n",\
-"// Copyright (C) 1993 - 2000 California Institute of Technology //\n",\
-"// //\n",\
-"// Read the COPYING and README files, or contact 'avida at alife.org', //\n",\
-"// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //\n",\
-"//////////////////////////////////////////////////////////////////////////////\n"]
-
-def modFiles( arg, dirname, name_list ):
- print "Entering %s\n" % dirname
- for ifile in name_list:
- dMatch = 0
- licMatch = 0
- filename = os.path.join(dirname, ifile)
- print filename,
- if ( os.path.isdir(filename) ):
- print "DIR"
- continue
-
- # Ignore non-source files
- if not sourceRE.search( ifile ):
- print "NOT SOURCE"
- continue
-
- lines = open( filename ).readlines()
- for iLine in range(len(lines)):
- # First try matching with the date line
- if dateRE.match( lines[iLine] ):
- lines[iLine] = cprString[1]
- dMatch = 1
-
- # Now try matching with the License line
- if licRE.match( lines[iLine] ):
- lines[iLine] = cprString[3]
- licMatch = 1
-
- nMatch = licMatch + dMatch
- print "%s %s" % (licMatch, dMatch),
- if( nMatch == 0 ):
- # The (C) lines aren't there, so add them
- lines[:0] = cprString
- elif (nMatch == 1):
- # If we only found one line skip this file (too weird)
- print
- continue
-
- # write out the altered version
- print "fixed"
- open( filename, 'w' ).writelines( lines )
-
-print 'Starting'
-os.path.walk( ".", modFiles, 1 )
More information about the Avida-cvs
mailing list