[Avida-SVN] r3523 - in branches/biounit: Avida.xcodeproj source/analyze source/classification
brysonda at myxo.css.msu.edu
brysonda at myxo.css.msu.edu
Thu Nov 5 14:23:24 PST 2009
Author: brysonda
Date: 2009-11-05 17:23:23 -0500 (Thu, 05 Nov 2009)
New Revision: 3523
Added:
branches/biounit/source/classification/cBGGenotype.cc
branches/biounit/source/classification/cBGGenotype.h
branches/biounit/source/classification/cBioGroupManager.cc
branches/biounit/source/classification/cBioGroupManager.h
Modified:
branches/biounit/Avida.xcodeproj/project.pbxproj
branches/biounit/source/analyze/cAnalyze.cc
branches/biounit/source/classification/cBioGroup.cc
branches/biounit/source/classification/cBioGroup.h
branches/biounit/source/classification/cBioUnit.cc
branches/biounit/source/classification/cBioUnit.h
Log:
Begin defining BioGroup and BioUnit. Add start of cBGGenotype (place-holder name to avoid conflict with current cGenotype).
Modified: branches/biounit/Avida.xcodeproj/project.pbxproj
===================================================================
--- branches/biounit/Avida.xcodeproj/project.pbxproj 2009-11-04 21:21:57 UTC (rev 3522)
+++ branches/biounit/Avida.xcodeproj/project.pbxproj 2009-11-05 22:23:23 UTC (rev 3523)
@@ -38,6 +38,10 @@
700D9C470F1A8F34002CC711 /* cModularityAnalysis.cc in Sources */ = {isa = PBXBuildFile; fileRef = 700D9C450F1A8F34002CC711 /* cModularityAnalysis.cc */; };
700E2996085A1F6000CF158A /* avida in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC3164D07626CF3008F7A48 /* avida */; };
700E2B87085DE54400CF158A /* avida-viewer in CopyFiles */ = {isa = PBXBuildFile; fileRef = 700E2B83085DE50C00CF158A /* avida-viewer */; };
+ 701E746B10A37967006B6193 /* cBGGenotype.h in Headers */ = {isa = PBXBuildFile; fileRef = 701E746910A37967006B6193 /* cBGGenotype.h */; };
+ 701E746C10A37967006B6193 /* cBGGenotype.cc in Sources */ = {isa = PBXBuildFile; fileRef = 701E746A10A37967006B6193 /* cBGGenotype.cc */; };
+ 701E748410A37DB2006B6193 /* cBioGroupManager.h in Headers */ = {isa = PBXBuildFile; fileRef = 701E748210A37DB2006B6193 /* cBioGroupManager.h */; };
+ 701E748510A37DB2006B6193 /* cBioGroupManager.cc in Sources */ = {isa = PBXBuildFile; fileRef = 701E748310A37DB2006B6193 /* cBioGroupManager.cc */; };
7020699C0FDFEB7900B77E39 /* cBitArray.cc in Sources */ = {isa = PBXBuildFile; fileRef = 7020828D0FB9F2DF00637AD6 /* cBitArray.cc */; };
7020828F0FB9F2DF00637AD6 /* cBitArray.cc in Sources */ = {isa = PBXBuildFile; fileRef = 7020828D0FB9F2DF00637AD6 /* cBitArray.cc */; };
702082900FB9F2DF00637AD6 /* cBitArray.h in Headers */ = {isa = PBXBuildFile; fileRef = 7020828E0FB9F2DF00637AD6 /* cBitArray.h */; };
@@ -464,6 +468,10 @@
701D9382094CBA69008B845F /* cDriverManager.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cDriverManager.cc; sourceTree = "<group>"; };
701D93E6094CBF71008B845F /* cDefaultAnalyzeDriver.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cDefaultAnalyzeDriver.h; sourceTree = "<group>"; };
701D93E7094CBF71008B845F /* cDefaultAnalyzeDriver.cc */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = cDefaultAnalyzeDriver.cc; sourceTree = "<group>"; };
+ 701E746910A37967006B6193 /* cBGGenotype.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cBGGenotype.h; sourceTree = "<group>"; };
+ 701E746A10A37967006B6193 /* cBGGenotype.cc */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = cBGGenotype.cc; sourceTree = "<group>"; };
+ 701E748210A37DB2006B6193 /* cBioGroupManager.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cBioGroupManager.h; sourceTree = "<group>"; };
+ 701E748310A37DB2006B6193 /* cBioGroupManager.cc */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = cBioGroupManager.cc; sourceTree = "<group>"; };
701EF27E0BEA5D2300DAE168 /* main.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = main.cc; sourceTree = "<group>"; };
7020828D0FB9F2DF00637AD6 /* cBitArray.cc */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = cBitArray.cc; sourceTree = "<group>"; };
7020828E0FB9F2DF00637AD6 /* cBitArray.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cBitArray.h; sourceTree = "<group>"; };
@@ -1525,6 +1533,10 @@
702244B8107D16010079CD25 /* cBioUnit.cc */,
702244C1107D168F0079CD25 /* cBioGroup.h */,
702244C2107D168F0079CD25 /* cBioGroup.cc */,
+ 701E746910A37967006B6193 /* cBGGenotype.h */,
+ 701E746A10A37967006B6193 /* cBGGenotype.cc */,
+ 701E748210A37DB2006B6193 /* cBioGroupManager.h */,
+ 701E748310A37DB2006B6193 /* cBioGroupManager.cc */,
);
path = classification;
sourceTree = "<group>";
@@ -1935,6 +1947,8 @@
702082900FB9F2DF00637AD6 /* cBitArray.h in Headers */,
702244B9107D16010079CD25 /* cBioUnit.h in Headers */,
702244C3107D168F0079CD25 /* cBioGroup.h in Headers */,
+ 701E746B10A37967006B6193 /* cBGGenotype.h in Headers */,
+ 701E748410A37DB2006B6193 /* cBioGroupManager.h in Headers */,
);
runOnlyForDeploymentPostprocessing = 0;
};
@@ -2319,6 +2333,8 @@
42C27C870FDC22AC00C45B78 /* cDemeTopologyNetwork.cc in Sources */,
702244BA107D16010079CD25 /* cBioUnit.cc in Sources */,
702244C4107D168F0079CD25 /* cBioGroup.cc in Sources */,
+ 701E746C10A37967006B6193 /* cBGGenotype.cc in Sources */,
+ 701E748510A37DB2006B6193 /* cBioGroupManager.cc in Sources */,
);
runOnlyForDeploymentPostprocessing = 0;
};
Modified: branches/biounit/source/analyze/cAnalyze.cc
===================================================================
--- branches/biounit/source/analyze/cAnalyze.cc 2009-11-04 21:21:57 UTC (rev 3522)
+++ branches/biounit/source/analyze/cAnalyze.cc 2009-11-05 22:23:23 UTC (rev 3523)
@@ -65,7 +65,6 @@
#include "cResource.h"
#include "cResourceHistory.h"
#include "cSchedule.h"
-#include "cSpecies.h"
#include "cStringIterator.h"
#include "cTestCPU.h"
#include "cWorld.h"
Added: branches/biounit/source/classification/cBGGenotype.cc
===================================================================
--- branches/biounit/source/classification/cBGGenotype.cc (rev 0)
+++ branches/biounit/source/classification/cBGGenotype.cc 2009-11-05 22:23:23 UTC (rev 3523)
@@ -0,0 +1,26 @@
+/*
+ * cBGGenotype.cc
+ * Avida
+ *
+ * Created by David on 11/5/09.
+ * Copyright 2009 Michigan State University. All rights reserved.
+ *
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; version 2
+ * of the License.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+ *
+ */
+
+#include "cBGGenotype.h"
+
Added: branches/biounit/source/classification/cBGGenotype.h
===================================================================
--- branches/biounit/source/classification/cBGGenotype.h (rev 0)
+++ branches/biounit/source/classification/cBGGenotype.h 2009-11-05 22:23:23 UTC (rev 3523)
@@ -0,0 +1,48 @@
+/*
+ * cBGGenotype.h
+ * Avida
+ *
+ * Created by David on 11/5/09.
+ * Copyright 2009 Michigan State University. All rights reserved.
+ *
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; version 2
+ * of the License.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+ *
+ */
+
+#ifndef cBGGenotype_h
+#define cBGGenotype_h
+
+#ifndef cBioGroup_h
+#include "cBioGroup.h"
+#endif
+
+class cBGGenotype : public cBioGroup
+{
+private:
+ cWorld* m_world;
+
+ cMetaGenome m_genome;
+ cString m_name;
+
+
+ cBGGenotype() { ; }
+
+public:
+ ~cBGGenotype() { ; }
+
+};
+
+#endif
Modified: branches/biounit/source/classification/cBioGroup.cc
===================================================================
--- branches/biounit/source/classification/cBioGroup.cc 2009-11-04 21:21:57 UTC (rev 3522)
+++ branches/biounit/source/classification/cBioGroup.cc 2009-11-05 22:23:23 UTC (rev 3523)
@@ -24,3 +24,4 @@
#include "cBioGroup.h"
+cBioGroup::~cBioGroup() { ; }
Modified: branches/biounit/source/classification/cBioGroup.h
===================================================================
--- branches/biounit/source/classification/cBioGroup.h 2009-11-04 21:21:57 UTC (rev 3522)
+++ branches/biounit/source/classification/cBioGroup.h 2009-11-05 22:23:23 UTC (rev 3523)
@@ -29,10 +29,21 @@
#include "cBioUnit.h"
#endif
+template<typename T> class tArray;
class cBioGroup
{
+public:
+ cBioGroup() { ; }
+ virtual ~cBioGroup() = 0;
+ virtual cBioGroup* ClassifyNewBioUnit(cBioUnit* bu, tArray<cBioGroups>* parents = NULL) = 0;
+ virtual void RemoveBioUnit(cBioUnit* bu) = 0;
+
+
+
+protected:
+
};
#endif
Added: branches/biounit/source/classification/cBioGroupManager.cc
===================================================================
--- branches/biounit/source/classification/cBioGroupManager.cc (rev 0)
+++ branches/biounit/source/classification/cBioGroupManager.cc 2009-11-05 22:23:23 UTC (rev 3523)
@@ -0,0 +1,26 @@
+/*
+ * cBioGroupManager.cc
+ * Avida
+ *
+ * Created by David on 11/5/09.
+ * Copyright 2009 Michigan State University. All rights reserved.
+ *
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; version 2
+ * of the License.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+ *
+ */
+
+#include "cBioGroupManager.h"
+
Added: branches/biounit/source/classification/cBioGroupManager.h
===================================================================
--- branches/biounit/source/classification/cBioGroupManager.h (rev 0)
+++ branches/biounit/source/classification/cBioGroupManager.h 2009-11-05 22:23:23 UTC (rev 3523)
@@ -0,0 +1,31 @@
+/*
+ * cBioGroupManager.h
+ * Avida
+ *
+ * Created by David on 11/5/09.
+ * Copyright 2009 Michigan State University. All rights reserved.
+ *
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; version 2
+ * of the License.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+ *
+ */
+
+#ifndef cBioGroupManager_h
+#define cBioGroupManager_h
+
+
+
+
+#endif
Modified: branches/biounit/source/classification/cBioUnit.cc
===================================================================
--- branches/biounit/source/classification/cBioUnit.cc 2009-11-04 21:21:57 UTC (rev 3522)
+++ branches/biounit/source/classification/cBioUnit.cc 2009-11-05 22:23:23 UTC (rev 3523)
@@ -24,3 +24,4 @@
#include "cBioUnit.h"
+cBioUnit::~cBioUnit() { ; }
\ No newline at end of file
Modified: branches/biounit/source/classification/cBioUnit.h
===================================================================
--- branches/biounit/source/classification/cBioUnit.h 2009-11-04 21:21:57 UTC (rev 3522)
+++ branches/biounit/source/classification/cBioUnit.h 2009-11-05 22:23:23 UTC (rev 3523)
@@ -25,11 +25,15 @@
#ifndef cBioUnit_h
#define cBioUnit_h
+class cMetaGenome;
+
class cBioUnit
{
+public:
+ cBioUnit() { ; }
+ virtual ~cBioUnit() = 0;
-
+ virtual cMetaGenome& GetMetaGenome() = 0;
};
-
#endif
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