[Avida-cvs] [avida-svn] r608 - in development: . Avida.xcodeproj source source/cpu source/main support support/config
brysonda@myxo.css.msu.edu
brysonda at myxo.css.msu.edu
Thu Apr 13 06:33:16 PDT 2006
Author: brysonda
Date: 2006-04-13 09:33:15 -0400 (Thu, 13 Apr 2006)
New Revision: 608
Added:
development/support/config/
development/support/config/CMakeLists.txt
development/support/config/SConscript
development/support/config/analyze.cfg
development/support/config/avida-smt.cfg
development/support/config/avida.cfg
development/support/config/environment.cfg
development/support/config/events.cfg
development/support/config/inst_set.4stack
development/support/config/inst_set.default
development/support/config/inst_set.sex
development/support/config/inst_set.smt
development/support/config/misc/
development/support/config/organism.default
development/support/config/organism.sex
development/support/config/organism.smt
development/support/config/organism.smtx
development/support/config/preset_organisms/
Removed:
development/avida_doc.rules
development/source/support/
Modified:
development/Avida.xcodeproj/project.pbxproj
development/CMakeLists.txt
development/source/cpu/cHardwareSMT.cc
development/source/main/cOrganism.cc
Log:
NOTE: FIXED build with CMAKE > 2.0! The problem was the result of defining the executable and library output paths based on the project binary directory BEFORE the project was defined. Newer versions of CMake were *correctly* setting these using an empty PROJECT_BINARY_DIR value. The definitions have been moved to have them properly assigned. Also, moved various support files out of source and into support.
Modified: development/Avida.xcodeproj/project.pbxproj
===================================================================
--- development/Avida.xcodeproj/project.pbxproj 2006-04-13 01:54:05 UTC (rev 607)
+++ development/Avida.xcodeproj/project.pbxproj 2006-04-13 13:33:15 UTC (rev 608)
@@ -13,29 +13,11 @@
7005A70609BA0FA90007E16E /* cTestCPUInterface.cc in Sources */ = {isa = PBXBuildFile; fileRef = 7005A70209BA0FA90007E16E /* cTestCPUInterface.cc */; };
7005A70809BA0FA90007E16E /* cTestCPUInterface.cc in Sources */ = {isa = PBXBuildFile; fileRef = 7005A70209BA0FA90007E16E /* cTestCPUInterface.cc */; };
7005A83209BA621F0007E16E /* cOrgMessage.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70B0868808F49EA800FC65FE /* cOrgMessage.cc */; };
- 700AEB7C09E3490400A073FD /* avida-smt.cfg in CopyFiles */ = {isa = PBXBuildFile; fileRef = 700AEB7B09E3490300A073FD /* avida-smt.cfg */; };
- 700AEB7D09E3490400A073FD /* avida-smt.cfg in CopyFiles */ = {isa = PBXBuildFile; fileRef = 700AEB7B09E3490300A073FD /* avida-smt.cfg */; };
- 700AEB7E09E3490400A073FD /* avida-smt.cfg in CopyFiles */ = {isa = PBXBuildFile; fileRef = 700AEB7B09E3490300A073FD /* avida-smt.cfg */; };
700E2996085A1F6000CF158A /* avida in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC3164D07626CF3008F7A48 /* avida */; };
700E2AF8085DE50C00CF158A /* avida.cc in Sources */ = {isa = PBXBuildFile; fileRef = DCC3109C0762539E008F7A48 /* avida.cc */; };
- 700E2B6F085DE50C00CF158A /* analyze.cfg in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC3114B0762539E008F7A48 /* analyze.cfg */; };
- 700E2B70085DE50C00CF158A /* environment.cfg in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC311800762539F008F7A48 /* environment.cfg */; };
- 700E2B71085DE50C00CF158A /* events.cfg in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC311810762539F008F7A48 /* events.cfg */; };
- 700E2B74085DE50C00CF158A /* inst_set.4stack in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC311840762539F008F7A48 /* inst_set.4stack */; };
- 700E2B75085DE50C00CF158A /* inst_set.default in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC311850762539F008F7A48 /* inst_set.default */; };
- 700E2B76085DE50C00CF158A /* organism.default in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC311890762539F008F7A48 /* organism.default */; };
- 700E2B78085DE50C00CF158A /* dummy in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC311950762539F008F7A48 /* dummy */; };
- 700E2B79085DE50C00CF158A /* organism.4stack in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC311970762539F008F7A48 /* organism.4stack */; };
- 700E2B7A085DE50C00CF158A /* organism.parasite in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC311980762539F008F7A48 /* organism.parasite */; };
- 700E2B7B085DE50C00CF158A /* organism.smt in CopyFiles */ = {isa = PBXBuildFile; fileRef = 706D330E0854A7B900D7DC8F /* organism.smt */; };
- 700E2B7D085DE50C00CF158A /* inst_set.smt in CopyFiles */ = {isa = PBXBuildFile; fileRef = 706D33270854A90D00D7DC8F /* inst_set.smt */; };
700E2B87085DE54400CF158A /* avida-viewer in CopyFiles */ = {isa = PBXBuildFile; fileRef = 700E2B83085DE50C00CF158A /* avida-viewer */; };
- 701384340900A45B0087ED2E /* organism.smtx in CopyFiles */ = {isa = PBXBuildFile; fileRef = 701384330900A45B0087ED2E /* organism.smtx */; };
- 701384350900A45B0087ED2E /* organism.smtx in CopyFiles */ = {isa = PBXBuildFile; fileRef = 701384330900A45B0087ED2E /* organism.smtx */; };
7013846209028B3E0087ED2E /* cAvidaConfig.cc in Sources */ = {isa = PBXBuildFile; fileRef = 7013846009028B3E0087ED2E /* cAvidaConfig.cc */; };
7013846409028B3E0087ED2E /* cAvidaConfig.cc in Sources */ = {isa = PBXBuildFile; fileRef = 7013846009028B3E0087ED2E /* cAvidaConfig.cc */; };
- 7013852D0902E36B0087ED2E /* avida.cfg in CopyFiles */ = {isa = PBXBuildFile; fileRef = 7013852C0902E36B0087ED2E /* avida.cfg */; };
- 7013852E0902E36B0087ED2E /* avida.cfg in CopyFiles */ = {isa = PBXBuildFile; fileRef = 7013852C0902E36B0087ED2E /* avida.cfg */; };
701D51CF09C645F50009B4F8 /* cAvidaContext.h in CopyFiles */ = {isa = PBXBuildFile; fileRef = 701D51CB09C645F50009B4F8 /* cAvidaContext.h */; };
701D51D109C645F50009B4F8 /* cAvidaContext.h in CopyFiles */ = {isa = PBXBuildFile; fileRef = 701D51CB09C645F50009B4F8 /* cAvidaContext.h */; };
701D915D094B864A008B845F /* cFallbackWorldDriver.cc in Sources */ = {isa = PBXBuildFile; fileRef = 701D915C094B864A008B845F /* cFallbackWorldDriver.cc */; };
@@ -67,12 +49,6 @@
70422A34091B141000A5E67F /* cAnalyze.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70422A1C091B141000A5E67F /* cAnalyze.cc */; };
70422A3C091B141000A5E67F /* cAnalyzeGenotype.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70422A24091B141000A5E67F /* cAnalyzeGenotype.cc */; };
70422A3E091B141000A5E67F /* cAnalyzeUtil.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70422A26091B141000A5E67F /* cAnalyzeUtil.cc */; };
- 70486BA00826722F009328F0 /* analyze.cfg in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC3114B0762539E008F7A48 /* analyze.cfg */; };
- 70486BA10826722F009328F0 /* environment.cfg in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC311800762539F008F7A48 /* environment.cfg */; };
- 70486BA20826722F009328F0 /* events.cfg in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC311810762539F008F7A48 /* events.cfg */; };
- 70486BA50826722F009328F0 /* inst_set.4stack in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC311840762539F008F7A48 /* inst_set.4stack */; };
- 70486BA60826722F009328F0 /* inst_set.default in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC311850762539F008F7A48 /* inst_set.default */; };
- 70486BA70826722F009328F0 /* organism.default in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC311890762539F008F7A48 /* organism.default */; };
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 */; };
@@ -106,11 +82,6 @@
7054A1B809A810CB00038658 /* cAnalyzeJobWorker.cc in Sources */ = {isa = PBXBuildFile; fileRef = 7054A1B409A810CB00038658 /* cAnalyzeJobWorker.cc */; };
7054A1BA09A810CB00038658 /* cAnalyzeJobWorker.cc in Sources */ = {isa = PBXBuildFile; fileRef = 7054A1B409A810CB00038658 /* cAnalyzeJobWorker.cc */; };
70658C5A085DF67D00486BED /* libncurses.5.4.dylib in Frameworks */ = {isa = PBXBuildFile; fileRef = 70658C59085DF67D00486BED /* libncurses.5.4.dylib */; };
- 706D32E90854A39800D7DC8F /* dummy in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC311950762539F008F7A48 /* dummy */; };
- 706D32EA0854A39900D7DC8F /* organism.4stack in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC311970762539F008F7A48 /* organism.4stack */; };
- 706D32EB0854A39900D7DC8F /* organism.parasite in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC311980762539F008F7A48 /* organism.parasite */; };
- 706D330F0854A7B900D7DC8F /* organism.smt in CopyFiles */ = {isa = PBXBuildFile; fileRef = 706D330E0854A7B900D7DC8F /* organism.smt */; };
- 706D33280854A90D00D7DC8F /* inst_set.smt in CopyFiles */ = {isa = PBXBuildFile; fileRef = 706D33270854A90D00D7DC8F /* inst_set.smt */; };
7073165D097C6C8F00815164 /* cParser.cc in Sources */ = {isa = PBXBuildFile; fileRef = 7073165B097C6C8F00815164 /* cParser.cc */; };
70731665097C6DF500815164 /* cASLibrary.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70731663097C6DF500815164 /* cASLibrary.cc */; };
7073166B097C6E0C00815164 /* cASSymbol.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70731669097C6E0C00815164 /* cASSymbol.cc */; };
@@ -382,19 +353,6 @@
70DCAD03097AF7CC002F8733 /* cDefaultRunDriver.cc in Sources */ = {isa = PBXBuildFile; fileRef = 701D930C094CAD6B008B845F /* cDefaultRunDriver.cc */; };
70DCAD04097AF7CC002F8733 /* cDriverManager.cc in Sources */ = {isa = PBXBuildFile; fileRef = 701D9382094CBA69008B845F /* cDriverManager.cc */; };
70DCAD05097AF7CC002F8733 /* cDefaultAnalyzeDriver.cc in Sources */ = {isa = PBXBuildFile; fileRef = 701D93E7094CBF71008B845F /* cDefaultAnalyzeDriver.cc */; };
- 70DCAD0A097AF7CC002F8733 /* analyze.cfg in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC3114B0762539E008F7A48 /* analyze.cfg */; };
- 70DCAD0B097AF7CC002F8733 /* environment.cfg in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC311800762539F008F7A48 /* environment.cfg */; };
- 70DCAD0C097AF7CC002F8733 /* events.cfg in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC311810762539F008F7A48 /* events.cfg */; };
- 70DCAD0D097AF7CC002F8733 /* inst_set.4stack in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC311840762539F008F7A48 /* inst_set.4stack */; };
- 70DCAD0E097AF7CC002F8733 /* inst_set.default in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC311850762539F008F7A48 /* inst_set.default */; };
- 70DCAD0F097AF7CC002F8733 /* organism.default in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC311890762539F008F7A48 /* organism.default */; };
- 70DCAD10097AF7CC002F8733 /* dummy in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC311950762539F008F7A48 /* dummy */; };
- 70DCAD11097AF7CC002F8733 /* organism.4stack in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC311970762539F008F7A48 /* organism.4stack */; };
- 70DCAD12097AF7CC002F8733 /* organism.parasite in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC311980762539F008F7A48 /* organism.parasite */; };
- 70DCAD13097AF7CC002F8733 /* organism.smt in CopyFiles */ = {isa = PBXBuildFile; fileRef = 706D330E0854A7B900D7DC8F /* organism.smt */; };
- 70DCAD14097AF7CC002F8733 /* inst_set.smt in CopyFiles */ = {isa = PBXBuildFile; fileRef = 706D33270854A90D00D7DC8F /* inst_set.smt */; };
- 70DCAD15097AF7CC002F8733 /* organism.smtx in CopyFiles */ = {isa = PBXBuildFile; fileRef = 701384330900A45B0087ED2E /* organism.smtx */; };
- 70DCAD16097AF7CC002F8733 /* avida.cfg in CopyFiles */ = {isa = PBXBuildFile; fileRef = 7013852C0902E36B0087ED2E /* avida.cfg */; };
70DCAD25097AF81A002F8733 /* cLexer.l in Sources */ = {isa = PBXBuildFile; fileRef = 70DCAD21097AF81A002F8733 /* cLexer.l */; };
70DCAD2F097AF8BC002F8733 /* main.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70DCAC57097AF730002F8733 /* main.cc */; };
70DCF66C09D4DE6500924128 /* libtcmalloc.a in Frameworks */ = {isa = PBXBuildFile; fileRef = 70AA941909D486AE006A24C8 /* libtcmalloc.a */; };
@@ -467,19 +425,6 @@
dstSubfolderSpec = 16;
files = (
700E2B87085DE54400CF158A /* avida-viewer in CopyFiles */,
- 700E2B6F085DE50C00CF158A /* analyze.cfg in CopyFiles */,
- 700E2B70085DE50C00CF158A /* environment.cfg in CopyFiles */,
- 700E2B71085DE50C00CF158A /* events.cfg in CopyFiles */,
- 700E2B74085DE50C00CF158A /* inst_set.4stack in CopyFiles */,
- 700E2B75085DE50C00CF158A /* inst_set.default in CopyFiles */,
- 700E2B76085DE50C00CF158A /* organism.default in CopyFiles */,
- 700E2B78085DE50C00CF158A /* dummy in CopyFiles */,
- 700E2B79085DE50C00CF158A /* organism.4stack in CopyFiles */,
- 700E2B7A085DE50C00CF158A /* organism.parasite in CopyFiles */,
- 700E2B7B085DE50C00CF158A /* organism.smt in CopyFiles */,
- 700E2B7D085DE50C00CF158A /* inst_set.smt in CopyFiles */,
- 701384340900A45B0087ED2E /* organism.smtx in CopyFiles */,
- 7013852E0902E36B0087ED2E /* avida.cfg in CopyFiles */,
701D92E4094C9E6F008B845F /* cDriverManager.h in CopyFiles */,
701D930F094CAD6B008B845F /* cDefaultRunDriver.h in CopyFiles */,
701D93EA094CBF71008B845F /* cDefaultAnalyzeDriver.h in CopyFiles */,
@@ -489,7 +434,6 @@
7054A1B709A810CB00038658 /* cAnalyzeJobWorker.h in CopyFiles */,
7005A70509BA0FA90007E16E /* cTestCPUInterface.h in CopyFiles */,
701D51D109C645F50009B4F8 /* cAvidaContext.h in CopyFiles */,
- 700AEB7E09E3490400A073FD /* avida-smt.cfg in CopyFiles */,
);
runOnlyForDeploymentPostprocessing = 0;
};
@@ -500,20 +444,6 @@
dstSubfolderSpec = 16;
files = (
700E2996085A1F6000CF158A /* avida in CopyFiles */,
- 70486BA00826722F009328F0 /* analyze.cfg in CopyFiles */,
- 70486BA10826722F009328F0 /* environment.cfg in CopyFiles */,
- 70486BA20826722F009328F0 /* events.cfg in CopyFiles */,
- 70486BA50826722F009328F0 /* inst_set.4stack in CopyFiles */,
- 70486BA60826722F009328F0 /* inst_set.default in CopyFiles */,
- 70486BA70826722F009328F0 /* organism.default in CopyFiles */,
- 706D32E90854A39800D7DC8F /* dummy in CopyFiles */,
- 706D32EA0854A39900D7DC8F /* organism.4stack in CopyFiles */,
- 706D32EB0854A39900D7DC8F /* organism.parasite in CopyFiles */,
- 706D330F0854A7B900D7DC8F /* organism.smt in CopyFiles */,
- 706D33280854A90D00D7DC8F /* inst_set.smt in CopyFiles */,
- 701384350900A45B0087ED2E /* organism.smtx in CopyFiles */,
- 7013852D0902E36B0087ED2E /* avida.cfg in CopyFiles */,
- 700AEB7C09E3490400A073FD /* avida-smt.cfg in CopyFiles */,
);
runOnlyForDeploymentPostprocessing = 0;
};
@@ -524,26 +454,12 @@
dstSubfolderSpec = 16;
files = (
702F532F0993060A00B2B507 /* avida-s in CopyFiles */,
- 70DCAD0A097AF7CC002F8733 /* analyze.cfg in CopyFiles */,
- 70DCAD0B097AF7CC002F8733 /* environment.cfg in CopyFiles */,
- 70DCAD0C097AF7CC002F8733 /* events.cfg in CopyFiles */,
- 70DCAD0D097AF7CC002F8733 /* inst_set.4stack in CopyFiles */,
- 70DCAD0E097AF7CC002F8733 /* inst_set.default in CopyFiles */,
- 70DCAD0F097AF7CC002F8733 /* organism.default in CopyFiles */,
- 70DCAD10097AF7CC002F8733 /* dummy in CopyFiles */,
- 70DCAD11097AF7CC002F8733 /* organism.4stack in CopyFiles */,
- 70DCAD12097AF7CC002F8733 /* organism.parasite in CopyFiles */,
- 70DCAD13097AF7CC002F8733 /* organism.smt in CopyFiles */,
- 70DCAD14097AF7CC002F8733 /* inst_set.smt in CopyFiles */,
- 70DCAD15097AF7CC002F8733 /* organism.smtx in CopyFiles */,
- 70DCAD16097AF7CC002F8733 /* avida.cfg in CopyFiles */,
7054A12009A7BEFC00038658 /* cThread.h in CopyFiles */,
7054A17009A8014600038658 /* cAnalyzeJobQueue.h in CopyFiles */,
7054A17A09A802BD00038658 /* cAnalyzeJob.h in CopyFiles */,
7054A1B509A810CB00038658 /* cAnalyzeJobWorker.h in CopyFiles */,
7005A70309BA0FA90007E16E /* cTestCPUInterface.h in CopyFiles */,
701D51CF09C645F50009B4F8 /* cAvidaContext.h in CopyFiles */,
- 700AEB7D09E3490400A073FD /* avida-smt.cfg in CopyFiles */,
);
runOnlyForDeploymentPostprocessing = 0;
};
@@ -554,14 +470,11 @@
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7005A70909BA0FBE0007E16E /* cOrgInterface.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cOrgInterface.h; sourceTree = "<group>"; };
700AE91B09DB65F200A073FD /* cTaskContext.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cTaskContext.h; sourceTree = "<group>"; };
- 700AEB7B09E3490300A073FD /* avida-smt.cfg */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = "avida-smt.cfg"; sourceTree = "<group>"; };
700E28CF0859FFD700CF158A /* tObjectFactory.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = tObjectFactory.h; sourceTree = "<group>"; };
700E2B83085DE50C00CF158A /* avida-viewer */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = "avida-viewer"; sourceTree = BUILT_PRODUCTS_DIR; };
- 701384330900A45B0087ED2E /* organism.smtx */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.smtx; sourceTree = "<group>"; };
7013845F09028B3E0087ED2E /* cAvidaConfig.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cAvidaConfig.h; sourceTree = "<group>"; };
7013846009028B3E0087ED2E /* cAvidaConfig.cc */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = cAvidaConfig.cc; sourceTree = "<group>"; };
701384A10902A16F0087ED2E /* defs.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = defs.h; sourceTree = "<group>"; };
- 7013852C0902E36B0087ED2E /* avida.cfg */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = avida.cfg; sourceTree = "<group>"; };
701D51CB09C645F50009B4F8 /* cAvidaContext.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cAvidaContext.h; sourceTree = "<group>"; };
701D9116094B773E008B845F /* cWorldDriver.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cWorldDriver.h; sourceTree = "<group>"; };
701D912B094B7AC1008B845F /* cAvidaDriver.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cAvidaDriver.h; sourceTree = "<group>"; };
@@ -631,8 +544,6 @@
7054A1B409A810CB00038658 /* cAnalyzeJobWorker.cc */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = cAnalyzeJobWorker.cc; sourceTree = "<group>"; };
70658C59085DF67D00486BED /* libncurses.5.4.dylib */ = {isa = PBXFileReference; lastKnownFileType = "compiled.mach-o.dylib"; name = libncurses.5.4.dylib; path = /usr/lib/libncurses.5.4.dylib; sourceTree = "<absolute>"; };
706D30CC0852328F00D7DC8F /* tInstLib.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = tInstLib.h; sourceTree = "<group>"; };
- 706D330E0854A7B900D7DC8F /* organism.smt */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = organism.smt; sourceTree = "<group>"; };
- 706D33270854A90D00D7DC8F /* inst_set.smt */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = inst_set.smt; sourceTree = "<group>"; };
7073165A097C6C8F00815164 /* cParser.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cParser.h; sourceTree = "<group>"; };
7073165B097C6C8F00815164 /* cParser.cc */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = cParser.cc; sourceTree = "<group>"; };
70731662097C6DF500815164 /* cASLibrary.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cASLibrary.h; sourceTree = "<group>"; };
@@ -646,6 +557,49 @@
707AF04409EAB529001AEA89 /* LandscapeActions.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = LandscapeActions.h; sourceTree = "<group>"; };
707AF04509EAB529001AEA89 /* LandscapeActions.cc */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = LandscapeActions.cc; sourceTree = "<group>"; };
707AF0F809EACC5E001AEA89 /* CMakeLists.txt */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = CMakeLists.txt; sourceTree = "<group>"; };
+ 707AF2D309EE8501001AEA89 /* analyze.cfg */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = analyze.cfg; sourceTree = "<group>"; };
+ 707AF2D409EE8501001AEA89 /* avida-smt.cfg */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = "avida-smt.cfg"; sourceTree = "<group>"; };
+ 707AF2D509EE8501001AEA89 /* avida.cfg */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = avida.cfg; sourceTree = "<group>"; };
+ 707AF2D609EE8501001AEA89 /* CMakeLists.txt */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = CMakeLists.txt; sourceTree = "<group>"; };
+ 707AF2D709EE8501001AEA89 /* environment.cfg */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = environment.cfg; sourceTree = "<group>"; };
+ 707AF2D809EE8501001AEA89 /* events.cfg */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = events.cfg; sourceTree = "<group>"; };
+ 707AF2D909EE8501001AEA89 /* inst_set.4stack */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.4stack; sourceTree = "<group>"; };
+ 707AF2DA09EE8501001AEA89 /* inst_set.default */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.default; sourceTree = "<group>"; };
+ 707AF2DB09EE8501001AEA89 /* inst_set.sex */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.sex; sourceTree = "<group>"; };
+ 707AF2DC09EE8501001AEA89 /* inst_set.smt */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.smt; sourceTree = "<group>"; };
+ 707AF2DE09EE8501001AEA89 /* environment.2paths */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = environment.2paths; sourceTree = "<group>"; };
+ 707AF2DF09EE8501001AEA89 /* environment.9resource */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = environment.9resource; sourceTree = "<group>"; };
+ 707AF2E009EE8501001AEA89 /* environment.all_logic */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = environment.all_logic; sourceTree = "<group>"; };
+ 707AF2E109EE8501001AEA89 /* environment.cascade */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = environment.cascade; sourceTree = "<group>"; };
+ 707AF2E209EE8501001AEA89 /* inst_set.19.short */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.19.short; sourceTree = "<group>"; };
+ 707AF2E309EE8501001AEA89 /* inst_set.24.old */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.24.old; sourceTree = "<group>"; };
+ 707AF2E409EE8501001AEA89 /* inst_set.26.default */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.26.default; sourceTree = "<group>"; };
+ 707AF2E509EE8501001AEA89 /* inst_set.27.multi */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.27.multi; sourceTree = "<group>"; };
+ 707AF2E609EE8501001AEA89 /* inst_set.27.no-nop */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = "inst_set.27.no-nop"; sourceTree = "<group>"; };
+ 707AF2E709EE8501001AEA89 /* inst_set.27.parasite */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.27.parasite; sourceTree = "<group>"; };
+ 707AF2E809EE8501001AEA89 /* inst_set.28.base */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.28.base; sourceTree = "<group>"; };
+ 707AF2E909EE8501001AEA89 /* inst_set.28.const */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.28.const; sourceTree = "<group>"; };
+ 707AF2EA09EE8501001AEA89 /* inst_set.29.base_memsize */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.29.base_memsize; sourceTree = "<group>"; };
+ 707AF2EB09EE8501001AEA89 /* inst_set.31.multi */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.31.multi; sourceTree = "<group>"; };
+ 707AF2EC09EE8501001AEA89 /* inst_set.32.heads */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.32.heads; sourceTree = "<group>"; };
+ 707AF2ED09EE8501001AEA89 /* inst_set.heads.parasite */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.heads.parasite; sourceTree = "<group>"; };
+ 707AF2EE09EE8501001AEA89 /* organism.heads.100 */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.heads.100; sourceTree = "<group>"; };
+ 707AF2EF09EE8501001AEA89 /* organism.heads.15 */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.heads.15; sourceTree = "<group>"; };
+ 707AF2F009EE8501001AEA89 /* organism.heads.50 */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.heads.50; sourceTree = "<group>"; };
+ 707AF2F109EE8501001AEA89 /* organism.host */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.host; sourceTree = "<group>"; };
+ 707AF2F209EE8501001AEA89 /* organism.host2 */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.host2; sourceTree = "<group>"; };
+ 707AF2F309EE8501001AEA89 /* organism.infected */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.infected; sourceTree = "<group>"; };
+ 707AF2F409EE8501001AEA89 /* organism.infected2 */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.infected2; sourceTree = "<group>"; };
+ 707AF2F509EE8501001AEA89 /* organism.noheads */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.noheads; sourceTree = "<group>"; };
+ 707AF2F609EE8501001AEA89 /* organism.default */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.default; sourceTree = "<group>"; };
+ 707AF2F709EE8501001AEA89 /* organism.sex */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.sex; sourceTree = "<group>"; };
+ 707AF2F809EE8501001AEA89 /* organism.smt */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.smt; sourceTree = "<group>"; };
+ 707AF2F909EE8501001AEA89 /* organism.smtx */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.smtx; sourceTree = "<group>"; };
+ 707AF2FB09EE8501001AEA89 /* CMakeLists.txt */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = CMakeLists.txt; sourceTree = "<group>"; };
+ 707AF2FC09EE8501001AEA89 /* dummy */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = dummy; sourceTree = "<group>"; };
+ 707AF2FD09EE8501001AEA89 /* organism.4stack */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.4stack; sourceTree = "<group>"; };
+ 707AF2FE09EE8501001AEA89 /* organism.parasite */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.parasite; sourceTree = "<group>"; };
+ 707AF2FF09EE8501001AEA89 /* SConscript */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = SConscript; sourceTree = "<group>"; };
7093DB4009D6F50300DE7FEB /* tSmartArray.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = tSmartArray.h; sourceTree = "<group>"; };
70AA941909D486AE006A24C8 /* libtcmalloc.a */ = {isa = PBXFileReference; explicitFileType = archive.ar; includeInIndex = 0; path = libtcmalloc.a; sourceTree = BUILT_PRODUCTS_DIR; };
70B0864808F4972600FC65FE /* cLandscape.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cLandscape.h; sourceTree = "<group>"; };
@@ -926,45 +880,6 @@
DCC30FEB0762539D008F7A48 /* CMakeLists.txt */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = CMakeLists.txt; sourceTree = "<group>"; };
DCC3109C0762539E008F7A48 /* avida.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = avida.cc; sourceTree = "<group>"; };
DCC310A90762539E008F7A48 /* CMakeLists.txt */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = CMakeLists.txt; sourceTree = "<group>"; };
- DCC3114B0762539E008F7A48 /* analyze.cfg */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = analyze.cfg; sourceTree = "<group>"; };
- DCC3114C0762539E008F7A48 /* CMakeLists.txt */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = CMakeLists.txt; sourceTree = "<group>"; };
- DCC311680762539E008F7A48 /* environment.2paths */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = environment.2paths; sourceTree = "<group>"; };
- DCC311690762539E008F7A48 /* environment.9resource */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = environment.9resource; sourceTree = "<group>"; };
- DCC3116A0762539E008F7A48 /* environment.all_logic */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = environment.all_logic; sourceTree = "<group>"; };
- DCC3116B0762539E008F7A48 /* environment.cascade */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = environment.cascade; sourceTree = "<group>"; };
- DCC3116C0762539E008F7A48 /* inst_set.19.short */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.19.short; sourceTree = "<group>"; };
- DCC3116D0762539E008F7A48 /* inst_set.24.old */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.24.old; sourceTree = "<group>"; };
- DCC3116E0762539E008F7A48 /* inst_set.26.default */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.26.default; sourceTree = "<group>"; };
- DCC3116F0762539E008F7A48 /* inst_set.27.multi */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.27.multi; sourceTree = "<group>"; };
- DCC311700762539E008F7A48 /* inst_set.27.no-nop */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = "inst_set.27.no-nop"; sourceTree = "<group>"; };
- DCC311710762539E008F7A48 /* inst_set.27.parasite */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.27.parasite; sourceTree = "<group>"; };
- DCC311720762539E008F7A48 /* inst_set.28.base */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.28.base; sourceTree = "<group>"; };
- DCC311730762539E008F7A48 /* inst_set.28.const */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.28.const; sourceTree = "<group>"; };
- DCC311740762539E008F7A48 /* inst_set.29.base_memsize */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.29.base_memsize; sourceTree = "<group>"; };
- DCC311750762539E008F7A48 /* inst_set.31.multi */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.31.multi; sourceTree = "<group>"; };
- DCC311760762539F008F7A48 /* inst_set.32.heads */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.32.heads; sourceTree = "<group>"; };
- DCC311770762539F008F7A48 /* inst_set.heads.parasite */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.heads.parasite; sourceTree = "<group>"; };
- DCC311780762539F008F7A48 /* organism.heads.100 */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.heads.100; sourceTree = "<group>"; };
- DCC311790762539F008F7A48 /* organism.heads.15 */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.heads.15; sourceTree = "<group>"; };
- DCC3117A0762539F008F7A48 /* organism.heads.50 */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.heads.50; sourceTree = "<group>"; };
- DCC3117B0762539F008F7A48 /* organism.host */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.host; sourceTree = "<group>"; };
- DCC3117C0762539F008F7A48 /* organism.host2 */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.host2; sourceTree = "<group>"; };
- DCC3117D0762539F008F7A48 /* organism.infected */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.infected; sourceTree = "<group>"; };
- DCC3117E0762539F008F7A48 /* organism.infected2 */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.infected2; sourceTree = "<group>"; };
- DCC3117F0762539F008F7A48 /* organism.noheads */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.noheads; sourceTree = "<group>"; };
- DCC311800762539F008F7A48 /* environment.cfg */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = environment.cfg; sourceTree = "<group>"; };
- DCC311810762539F008F7A48 /* events.cfg */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = events.cfg; sourceTree = "<group>"; };
- DCC311840762539F008F7A48 /* inst_set.4stack */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.4stack; sourceTree = "<group>"; };
- DCC311850762539F008F7A48 /* inst_set.default */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.default; sourceTree = "<group>"; };
- DCC311860762539F008F7A48 /* inst_set.sex */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.sex; sourceTree = "<group>"; };
- DCC311870762539F008F7A48 /* inst_set.tmp */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.tmp; sourceTree = "<group>"; };
- DCC311890762539F008F7A48 /* organism.default */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.default; sourceTree = "<group>"; };
- DCC3118A0762539F008F7A48 /* organism.heads.100 */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.heads.100; sourceTree = "<group>"; };
- DCC3118B0762539F008F7A48 /* organism.sex */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.sex; sourceTree = "<group>"; };
- DCC311940762539F008F7A48 /* CMakeLists.txt */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = CMakeLists.txt; sourceTree = "<group>"; };
- DCC311950762539F008F7A48 /* dummy */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = dummy; sourceTree = "<group>"; };
- DCC311970762539F008F7A48 /* organism.4stack */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.4stack; sourceTree = "<group>"; };
- DCC311980762539F008F7A48 /* organism.parasite */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.parasite; sourceTree = "<group>"; };
DCC31345076253A0008F7A48 /* CMakeLists.txt */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = CMakeLists.txt; sourceTree = "<group>"; };
DCC3143B076253A1008F7A48 /* CMakeLists.txt */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = CMakeLists.txt; sourceTree = "<group>"; };
DCC3143C076253A1008F7A48 /* compare.c */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.c; path = compare.c; sourceTree = "<group>"; };
@@ -1115,6 +1030,73 @@
path = actions;
sourceTree = "<group>";
};
+ 707AF2D209EE8501001AEA89 /* Support */ = {
+ isa = PBXGroup;
+ children = (
+ 707AF2D309EE8501001AEA89 /* analyze.cfg */,
+ 707AF2D409EE8501001AEA89 /* avida-smt.cfg */,
+ 707AF2D509EE8501001AEA89 /* avida.cfg */,
+ 707AF2D609EE8501001AEA89 /* CMakeLists.txt */,
+ 707AF2D709EE8501001AEA89 /* environment.cfg */,
+ 707AF2D809EE8501001AEA89 /* events.cfg */,
+ 707AF2D909EE8501001AEA89 /* inst_set.4stack */,
+ 707AF2DA09EE8501001AEA89 /* inst_set.default */,
+ 707AF2DB09EE8501001AEA89 /* inst_set.sex */,
+ 707AF2DC09EE8501001AEA89 /* inst_set.smt */,
+ 707AF2DD09EE8501001AEA89 /* misc */,
+ 707AF2F609EE8501001AEA89 /* organism.default */,
+ 707AF2F709EE8501001AEA89 /* organism.sex */,
+ 707AF2F809EE8501001AEA89 /* organism.smt */,
+ 707AF2F909EE8501001AEA89 /* organism.smtx */,
+ 707AF2FA09EE8501001AEA89 /* preset_organisms */,
+ 707AF2FF09EE8501001AEA89 /* SConscript */,
+ );
+ name = Support;
+ path = support/config;
+ sourceTree = "<group>";
+ };
+ 707AF2DD09EE8501001AEA89 /* misc */ = {
+ isa = PBXGroup;
+ children = (
+ 707AF2DE09EE8501001AEA89 /* environment.2paths */,
+ 707AF2DF09EE8501001AEA89 /* environment.9resource */,
+ 707AF2E009EE8501001AEA89 /* environment.all_logic */,
+ 707AF2E109EE8501001AEA89 /* environment.cascade */,
+ 707AF2E209EE8501001AEA89 /* inst_set.19.short */,
+ 707AF2E309EE8501001AEA89 /* inst_set.24.old */,
+ 707AF2E409EE8501001AEA89 /* inst_set.26.default */,
+ 707AF2E509EE8501001AEA89 /* inst_set.27.multi */,
+ 707AF2E609EE8501001AEA89 /* inst_set.27.no-nop */,
+ 707AF2E709EE8501001AEA89 /* inst_set.27.parasite */,
+ 707AF2E809EE8501001AEA89 /* inst_set.28.base */,
+ 707AF2E909EE8501001AEA89 /* inst_set.28.const */,
+ 707AF2EA09EE8501001AEA89 /* inst_set.29.base_memsize */,
+ 707AF2EB09EE8501001AEA89 /* inst_set.31.multi */,
+ 707AF2EC09EE8501001AEA89 /* inst_set.32.heads */,
+ 707AF2ED09EE8501001AEA89 /* inst_set.heads.parasite */,
+ 707AF2EE09EE8501001AEA89 /* organism.heads.100 */,
+ 707AF2EF09EE8501001AEA89 /* organism.heads.15 */,
+ 707AF2F009EE8501001AEA89 /* organism.heads.50 */,
+ 707AF2F109EE8501001AEA89 /* organism.host */,
+ 707AF2F209EE8501001AEA89 /* organism.host2 */,
+ 707AF2F309EE8501001AEA89 /* organism.infected */,
+ 707AF2F409EE8501001AEA89 /* organism.infected2 */,
+ 707AF2F509EE8501001AEA89 /* organism.noheads */,
+ );
+ path = misc;
+ sourceTree = "<group>";
+ };
+ 707AF2FA09EE8501001AEA89 /* preset_organisms */ = {
+ isa = PBXGroup;
+ children = (
+ 707AF2FB09EE8501001AEA89 /* CMakeLists.txt */,
+ 707AF2FC09EE8501001AEA89 /* dummy */,
+ 707AF2FD09EE8501001AEA89 /* organism.4stack */,
+ 707AF2FE09EE8501001AEA89 /* organism.parasite */,
+ );
+ path = preset_organisms;
+ sourceTree = "<group>";
+ };
70DCAC54097AF730002F8733 /* targets */ = {
isa = PBXGroup;
children = (
@@ -1267,7 +1249,7 @@
isa = PBXGroup;
children = (
DCC30C670762539A008F7A48 /* Main Source */,
- DCC3113A0762539E008F7A48 /* Support */,
+ 707AF2D209EE8501001AEA89 /* Support */,
DCC315B6076253A5008F7A48 /* Utilities */,
DCC3164E07626CF3008F7A48 /* Products */,
70FB86A908BFAFEC00BDF589 /* CMakeLists.txt */,
@@ -1460,74 +1442,6 @@
path = main;
sourceTree = "<group>";
};
- DCC3113A0762539E008F7A48 /* Support */ = {
- isa = PBXGroup;
- children = (
- 700AEB7B09E3490300A073FD /* avida-smt.cfg */,
- 701384330900A45B0087ED2E /* organism.smtx */,
- DCC3114B0762539E008F7A48 /* analyze.cfg */,
- DCC3114C0762539E008F7A48 /* CMakeLists.txt */,
- DCC3114D0762539E008F7A48 /* config */,
- DCC311800762539F008F7A48 /* environment.cfg */,
- DCC311810762539F008F7A48 /* events.cfg */,
- DCC311840762539F008F7A48 /* inst_set.4stack */,
- DCC311850762539F008F7A48 /* inst_set.default */,
- DCC311860762539F008F7A48 /* inst_set.sex */,
- 706D33270854A90D00D7DC8F /* inst_set.smt */,
- DCC311870762539F008F7A48 /* inst_set.tmp */,
- DCC311890762539F008F7A48 /* organism.default */,
- DCC3118A0762539F008F7A48 /* organism.heads.100 */,
- DCC3118B0762539F008F7A48 /* organism.sex */,
- 706D330E0854A7B900D7DC8F /* organism.smt */,
- DCC3118C0762539F008F7A48 /* preset_organisms */,
- 7013852C0902E36B0087ED2E /* avida.cfg */,
- );
- name = Support;
- path = source/support;
- sourceTree = "<group>";
- };
- DCC3114D0762539E008F7A48 /* config */ = {
- isa = PBXGroup;
- children = (
- DCC311680762539E008F7A48 /* environment.2paths */,
- DCC311690762539E008F7A48 /* environment.9resource */,
- DCC3116A0762539E008F7A48 /* environment.all_logic */,
- DCC3116B0762539E008F7A48 /* environment.cascade */,
- DCC3116C0762539E008F7A48 /* inst_set.19.short */,
- DCC3116D0762539E008F7A48 /* inst_set.24.old */,
- DCC3116E0762539E008F7A48 /* inst_set.26.default */,
- DCC3116F0762539E008F7A48 /* inst_set.27.multi */,
- DCC311700762539E008F7A48 /* inst_set.27.no-nop */,
- DCC311710762539E008F7A48 /* inst_set.27.parasite */,
- DCC311720762539E008F7A48 /* inst_set.28.base */,
- DCC311730762539E008F7A48 /* inst_set.28.const */,
- DCC311740762539E008F7A48 /* inst_set.29.base_memsize */,
- DCC311750762539E008F7A48 /* inst_set.31.multi */,
- DCC311760762539F008F7A48 /* inst_set.32.heads */,
- DCC311770762539F008F7A48 /* inst_set.heads.parasite */,
- DCC311780762539F008F7A48 /* organism.heads.100 */,
- DCC311790762539F008F7A48 /* organism.heads.15 */,
- DCC3117A0762539F008F7A48 /* organism.heads.50 */,
- DCC3117B0762539F008F7A48 /* organism.host */,
- DCC3117C0762539F008F7A48 /* organism.host2 */,
- DCC3117D0762539F008F7A48 /* organism.infected */,
- DCC3117E0762539F008F7A48 /* organism.infected2 */,
- DCC3117F0762539F008F7A48 /* organism.noheads */,
- );
- path = config;
- sourceTree = "<group>";
- };
- DCC3118C0762539F008F7A48 /* preset_organisms */ = {
- isa = PBXGroup;
- children = (
- DCC311940762539F008F7A48 /* CMakeLists.txt */,
- DCC311950762539F008F7A48 /* dummy */,
- DCC311970762539F008F7A48 /* organism.4stack */,
- DCC311980762539F008F7A48 /* organism.parasite */,
- );
- path = preset_organisms;
- sourceTree = "<group>";
- };
DCC31340076253A0008F7A48 /* third-party */ = {
isa = PBXGroup;
children = (
Modified: development/CMakeLists.txt
===================================================================
--- development/CMakeLists.txt 2006-04-13 01:54:05 UTC (rev 607)
+++ development/CMakeLists.txt 2006-04-13 13:33:15 UTC (rev 608)
@@ -60,10 +60,22 @@
"Choose the type of build, options are: None(CMAKE_CXX_FLAGS or CMAKE_C_FLAGS used) Debug Release RelWithDebInfo MinSizeRel."
)
-# Default location for installed software / configs / docs is work
-# subdirectory of build directory.
+
+# This section introduces the Avida project to CMake. In this file, it
+# must be between the configuration options above (otherwise it
+# overrides their defaults) and the configuration options, cmake module
+# includes, and convenience variables below (otherwise some variables
+# can't be properly defined because PROJECT_SOURCE_DIR and
+# PROJECT_BUILD_DIR aren't yet defined).
+
+PROJECT(AVIDA)
+SUBDIRS(source support)
+
+# The following three variables must be after the PROJECT statement, otherwise newer versions of cmake
+# will (correctly) use an empty value of PROJECT_BINARY_DIR, since the project didn't exist yet.
+
+# Default location for installed software / configs / docs is the build directory.
SET(CMAKE_INSTALL_PREFIX
- #"${PROJECT_BINARY_DIR}/work"
"${PROJECT_BINARY_DIR}"
CACHE PATH
"Install path prefix, prepended onto install directories."
@@ -76,24 +88,12 @@
"Single output directory for building all executables."
)
-
SET(LIBRARY_OUTPUT_PATH
"${PROJECT_BINARY_DIR}/lib"
CACHE PATH
"Built libraries are placed here before installation."
)
-
-# This section introduces the Avida project to CMake. In this file, it
-# must be between the configuration options above (otherwise it
-# overrides their defaults) and the configuration options, cmake module
-# includes, and convenience variables below (otherwise some variables
-# can't be properly defined because PROJECT_SOURCE_DIR and
-# PROJECT_BUILD_DIR aren't yet defined).
-
-PROJECT(AVIDA)
-SUBDIRS(source)
-
# Experimental Boost.Python interface to avida is disabled by default.
OPTION(AVD_PY_BINDINGS
"Enable Python interface to Avida. (EXPERIMENTAL)"
Deleted: development/avida_doc.rules
===================================================================
--- development/avida_doc.rules 2006-04-13 01:54:05 UTC (rev 607)
+++ development/avida_doc.rules 2006-04-13 13:33:15 UTC (rev 608)
@@ -1,29 +0,0 @@
-# start with:
-# makekdedoc --rule-file avida_doc.rules --srcdir . --outputdir doc
-# in directory source
-#
-# In order to put the documentation on the web, it has to be
-# copied to /home/httpd/html/avida/html/doc_current on myxo.css.msu.edu.
-#
-#
-# documentation is generated for the following directories:
-doc_MODULES = tools cpu main event viewers
-
-# rules for tools
- tools_FILES = *.hh
-
-# rules for cpu
- cpu_FILES = *.hh
- cpu_LIBS = -ltools
-
-# rules for main
- main_FILES = *.hh
- main_LIBS = -ltools -lcpu
-
-# rules for event
- event_FILES = *.hh
- event_LIBS = -ltools -lcpu -lmain
-
-# rules for viewers
- viewers_FILES = *.hh
- viewers_LIBS = -ltools -lcpu -lmain
Modified: development/source/cpu/cHardwareSMT.cc
===================================================================
--- development/source/cpu/cHardwareSMT.cc 2006-04-13 01:54:05 UTC (rev 607)
+++ development/source/cpu/cHardwareSMT.cc 2006-04-13 13:33:15 UTC (rev 608)
@@ -692,57 +692,31 @@
const int end_pos = GetHead(nHardware::HEAD_WRITE).GetPosition();
const int mem_space_used = GetHead(nHardware::HEAD_WRITE).GetMemSpace();
- // Make sure the creature will still be above the minimum size,
- // TEMPORARY! INJECTED CODE CAN
+ // Make sure the creature will still be above the minimum size
if (end_pos <= 0) {
Fault(FAULT_LOC_INJECT, FAULT_TYPE_ERROR, "inject: no code to inject");
return false; // (inject fails)
}
-
if (end_pos < MIN_INJECT_SIZE) {
m_mem_array[mem_space_used] = cGenome("a");
Fault(FAULT_LOC_INJECT, FAULT_TYPE_ERROR, "inject: new size too small");
return false; // (inject fails)
- }
-
+ }
+
m_mem_array[mem_space_used].Resize(end_pos);
cCPUMemory injected_code = m_mem_array[mem_space_used];
Inject_DoMutations(ctx, mut_multiplier, injected_code);
- int inject_signal = false;
+ bool inject_signal = false;
+ if (injected_code.GetSize() > 0) inject_signal = organism->InjectParasite(injected_code);
- if(injected_code.GetSize() > 0)
- inject_signal = organism->InjectParasite(injected_code);
-
- //************* CALL GOES HERE ******************//
- // spin around randomly (caution: possible organism dizziness)
- //const int num_neighbors = organism->GetNeighborhoodSize();
- //for(unsigned int i=0; i<ctx.GetRandom().GetUInt(num_neighbors); i++)
- // organism->Rotate(1);
-
- // If we don't have a host, stop here.
- //cOrganism * host_organism = organism->GetNeighbor();
-
-
- //if(host_organism!=NULL)
- // {
- //
- // }
-
- //************** CALL ENDS HERE ******************//
-
//reset the memory space which was injected
m_mem_array[mem_space_used] = cGenome("a");
- for(int x=0; x<nHardware::NUM_HEADS; x++) {
- GetHead(x).Reset(IP().GetMemSpace(), this);
- }
-
- for(int x=0; x < nHardwareSMT::NUM_LOCAL_STACKS; x++) {
- Stack(x).Clear();
- }
+ for (int x = 0; x < nHardware::NUM_HEADS; x++) GetHead(x).Reset(IP().GetMemSpace(), this);
+ for (int x = 0; x < nHardwareSMT::NUM_LOCAL_STACKS; x++) Stack(x).Clear();
AdvanceIP() = false;
@@ -750,7 +724,7 @@
}
//This is the code run by the TARGET of an injection. This RECIEVES the infection.
-bool cHardwareSMT::InjectHost(const cCodeLabel & in_label, const cGenome & inject_code)
+bool cHardwareSMT::InjectHost(const cCodeLabel& in_label, const cGenome& inject_code)
{
// @DMB - Need to discuss how InjectHost should work with extensible memory spaces...
return false;
@@ -2008,8 +1982,9 @@
bool cHardwareSMT::Inst_Inject(cAvidaContext& ctx)
{
- double mut_multiplier = 1;
-
+ ReadLabel(nHardwareSMT::MAX_MEMSPACE_LABEL);
+
+ double mut_multiplier = 1.0;
return InjectParasite(ctx, mut_multiplier);
}
Modified: development/source/main/cOrganism.cc
===================================================================
--- development/source/main/cOrganism.cc 2006-04-13 01:54:05 UTC (rev 607)
+++ development/source/main/cOrganism.cc 2006-04-13 13:33:15 UTC (rev 608)
@@ -349,7 +349,7 @@
}
-bool cOrganism::InjectParasite(const cGenome & injected_code)
+bool cOrganism::InjectParasite(const cGenome& injected_code)
{
assert(m_interface);
return m_interface->InjectParasite(this, injected_code);
Copied: development/support/config/CMakeLists.txt (from rev 607, development/source/support/CMakeLists.txt)
===================================================================
--- development/source/support/CMakeLists.txt 2006-04-13 01:54:05 UTC (rev 607)
+++ development/support/config/CMakeLists.txt 2006-04-13 13:33:15 UTC (rev 608)
@@ -0,0 +1,17 @@
+SUBDIRS(preset_organisms)
+
+INSTALL_FILES(/work FILES
+ analyze.cfg
+ avida-smt.cfg
+ avida.cfg
+ environment.cfg
+ events.cfg
+ inst_set.4stack
+ inst_set.default
+ inst_set.sex
+ inst_set.smt
+ organism.default
+ organism.sex
+ organism.smt
+ organism.smtx
+)
Copied: development/support/config/SConscript (from rev 607, development/source/support/SConscript)
Copied: development/support/config/analyze.cfg (from rev 607, development/source/support/analyze.cfg)
Copied: development/support/config/avida-smt.cfg (from rev 607, development/source/support/avida-smt.cfg)
Copied: development/support/config/avida.cfg (from rev 607, development/source/support/avida.cfg)
Copied: development/support/config/environment.cfg (from rev 607, development/source/support/environment.cfg)
Copied: development/support/config/events.cfg (from rev 607, development/source/support/events.cfg)
Copied: development/support/config/inst_set.4stack (from rev 607, development/source/support/inst_set.4stack)
Copied: development/support/config/inst_set.default (from rev 607, development/source/support/inst_set.default)
Copied: development/support/config/inst_set.sex (from rev 607, development/source/support/inst_set.sex)
Copied: development/support/config/inst_set.smt (from rev 607, development/source/support/inst_set.smt)
Copied: development/support/config/misc (from rev 607, development/source/support/config)
Copied: development/support/config/organism.default (from rev 607, development/source/support/organism.default)
Copied: development/support/config/organism.sex (from rev 607, development/source/support/organism.sex)
Copied: development/support/config/organism.smt (from rev 607, development/source/support/organism.smt)
Copied: development/support/config/organism.smtx (from rev 607, development/source/support/organism.smtx)
Copied: development/support/config/preset_organisms (from rev 607, development/source/support/preset_organisms)
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