/dports/biology/avida/avida-2.12.4-src/avida-core/source/analyze/ |
H A D | cGenotypeBatch.cc | 42 cAnalyzeGenotype* genotype = NULL; in ~cGenotypeBatch() 77 return new cAnalyzeGenotype(*(m_list.FindMax(&cAnalyzeGenotype::GetNumCPUs))); in FindGenotypeNumCPUs() 89 return new cAnalyzeGenotype(*(m_list.FindMax(&cAnalyzeGenotype::GetTotalCPUs))); in FindGenotypeTotalCPUs() 101 return new cAnalyzeGenotype(*(m_list.FindMax(&cAnalyzeGenotype::GetMerit))); in FindGenotypeMetabolicRate() 113 return new cAnalyzeGenotype(*(m_list.FindMax(&cAnalyzeGenotype::GetFitness))); in FindGenotypeFitness() 125 return new cAnalyzeGenotype(*(m_list.FindValue(&cAnalyzeGenotype::GetID, gid))); in FindGenotypeID() 190 cAnalyzeGenotype* on_child = NULL; in FindLastCommonAncestor() 204 cAnalyzeGenotype* lca = NULL; in FindLastCommonAncestor() 205 cAnalyzeGenotype* test_lca = NULL; in FindLastCommonAncestor() 262 cAnalyzeGenotype* gen_p1 = NULL; in FindSexLineage() [all …]
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H A D | cGenotypeBatch.h | 35 class cAnalyzeGenotype; variable 40 tListPlus<cAnalyzeGenotype> m_list; 42 cAnalyzeGenotype* m_lineage_head; 43 cAnalyzeGenotype* m_clade_head; 69 cAnalyzeGenotype* FindGenotypeNumCPUs() const; 70 cAnalyzeGenotype* PopGenotypeNumCPUs(); 72 cAnalyzeGenotype* PopGenotypeTotalCPUs(); 74 cAnalyzeGenotype* PopGenotypeMetabolicRate(); 76 cAnalyzeGenotype* PopGenotypeFitness(); 78 cAnalyzeGenotype* PopGenotypeID(int gid); [all …]
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H A D | cAnalyzeGenotype.cc | 52 cAnalyzeGenotype::cAnalyzeGenotype(cWorld* world, const Genome& genome) in cAnalyzeGenotype() function in cAnalyzeGenotype 101 cAnalyzeGenotype::cAnalyzeGenotype(const cAnalyzeGenotype& _gen) in cAnalyzeGenotype() function in cAnalyzeGenotype 155 cAnalyzeGenotype::~cAnalyzeGenotype() in ~cAnalyzeGenotype() 169 tDataCommandManager<cAnalyzeGenotype>* cAnalyzeGenotype::buildDataCommandManager() in buildDataCommandManager() 171 tDataCommandManager<cAnalyzeGenotype>* dcm = new tDataCommandManager<cAnalyzeGenotype>; in buildDataCommandManager() 183 (KEYWORD, DESC, &cAnalyzeGenotype::GET, &cAnalyzeGenotype::SET, COMP, null_str, html_str)); \ in buildDataCommandManager() 294 ("task", &cAnalyzeGenotype::DescTask, &cAnalyzeGenotype::GetTaskCount, 5)); in buildDataCommandManager() 302 ("r_tot", &cAnalyzeGenotype::DescRTot, &cAnalyzeGenotype::GetRBinTotal)); in buildDataCommandManager() 304 ("r_avail", &cAnalyzeGenotype::DescRAvail, &cAnalyzeGenotype::GetRBinAvail)); in buildDataCommandManager() 308 ("r_spec", &cAnalyzeGenotype::DescRSpec, &cAnalyzeGenotype::GetRSpec)); in buildDataCommandManager() [all …]
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H A D | cModularityAnalysis.h | 36 class cAnalyzeGenotype; variable 44 cAnalyzeGenotype* m_genotype; 53 static cFlexVar GetTasksDoneFor(const cAnalyzeGenotype* genotype); 54 static cFlexVar GetInstsInvolvedInTasksFor(const cAnalyzeGenotype* genotype); 55 static cFlexVar GetTaskProportionFor(const cAnalyzeGenotype* genotype); 56 static cFlexVar GetAveTasksPerSiteFor(const cAnalyzeGenotype* genotype); 57 static cFlexVar GetAveSitesPerTaskFor(const cAnalyzeGenotype* genotype); 58 static cFlexVar GetPropNonoverlapFor(const cAnalyzeGenotype* genotype); 61 static cString DescSitesPerTask(const cAnalyzeGenotype* genotype, int idx); 64 static cFlexVar GetTaskLengthFor(const cAnalyzeGenotype* genotype, int idx); [all …]
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H A D | cAnalyzeTreeStats_Gamma.h | 34 class cAnalyzeGenotype; variable 49 cAnalyzeGenotype *m_parent; 50 cAnalyzeGenotype *m_first_child; 51 cAnalyzeGenotype *m_second_child; 54 cAnalyzeGenotype *parent = 0, 55 cAnalyzeGenotype *first_child = 0, 56 cAnalyzeGenotype *second_child = 0 75 tArray<cAnalyzeGenotype *> &lineage, 80 tArray<cAnalyzeGenotype *> &lineage, 84 tArray<cAnalyzeGenotype *> &lineage, [all …]
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H A D | cAnalyzeGenotype.h | 76 class cAnalyzeGenotype; variable 84 cAnalyzeGenotype *m_parent; 85 tList<cAnalyzeGenotype> m_child_list; 93 cAnalyzeGenotype* FindChild(cAnalyzeGenotype* child) { return GetChildList().FindPtr(child); } in FindChild() 94 cAnalyzeGenotype* RemoveChild(cAnalyzeGenotype* child) { return GetChildList().Remove(child); } in RemoveChild() 99 class cAnalyzeGenotype 246 cAnalyzeGenotype(const cAnalyzeGenotype& _gen); 247 ~cAnalyzeGenotype(); 566 bool UnlinkChild(cAnalyzeGenotype &child) in UnlinkChild() 579 friend class cAnalyzeGenotype; variable [all …]
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H A D | cAnalyzeTreeStats_Gamma.cc | 37 cAnalyzeGenotype a(**((cAnalyzeGenotype**)_a)); in CompareAGPhyloDepth() 38 cAnalyzeGenotype b(**((cAnalyzeGenotype**)_b)); in CompareAGPhyloDepth() 44 cAnalyzeGenotype a(**((cAnalyzeGenotype**)_a)); in CompareAGUpdateBorn() 45 cAnalyzeGenotype b(**((cAnalyzeGenotype**)_b)); in CompareAGUpdateBorn() 64 cAnalyzeGenotype *parent, in cAnalyzeLineageFurcation() 65 cAnalyzeGenotype *first_child, in cAnalyzeLineageFurcation() 66 cAnalyzeGenotype *second_child in cAnalyzeLineageFurcation() 104 cAnalyzeGenotype * genotype = NULL; in LoadGenotypes() 117 tArray<cAnalyzeGenotype *> &lineage, in MapIDToGenotypePos() 133 tArray<cAnalyzeGenotype *> &lineage, in EstablishLinks() [all …]
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H A D | cModularityAnalysis.cc | 33 tDataCommandManager<cAnalyzeGenotype>& dcm = cAnalyzeGenotype::GetDataCommandManager(); in Initialize() 36 dcm.Add(KEYWORD, new tDataEntryProxy<cAnalyzeGenotype, cFlexVar ()> \ in Initialize() 39 dcm.Add(KEYWORD, new tDataEntryProxy<cAnalyzeGenotype, cFlexVar (int)> \ in Initialize() 224 cAnalyzeGenotype::ReadToken* tok = genotype->GetReadToken(); \ 229 cAnalyzeGenotype::ReadToken* tok = genotype->GetReadToken(); \ 234 cFlexVar cModularityAnalysis::GetTasksDoneFor(const cAnalyzeGenotype* genotype) in GetTasksDoneFor() 248 cFlexVar cModularityAnalysis::GetTaskProportionFor(const cAnalyzeGenotype* genotype) in GetTaskProportionFor() 255 cFlexVar cModularityAnalysis::GetAveTasksPerSiteFor(const cAnalyzeGenotype* genotype) in GetAveTasksPerSiteFor() 262 cFlexVar cModularityAnalysis::GetAveSitesPerTaskFor(const cAnalyzeGenotype* genotype) in GetAveSitesPerTaskFor() 269 cFlexVar cModularityAnalysis::GetPropNonoverlapFor(const cAnalyzeGenotype* genotype) in GetPropNonoverlapFor() [all …]
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H A D | cAnalyze.cc | 190 cAnalyzeGenotype* genotype = new cAnalyzeGenotype(m_world, genome); in LoadOrganism() 220 cAnalyzeGenotype* genotype = new cAnalyzeGenotype(m_world, genome); in LoadSequence() 777 cAnalyzeGenotype* genotype = new cAnalyzeGenotype(m_world, default_genome); in LoadFile() 1091 cAnalyzeGenotype * found_dad; in FindSexLineage() 1092 cAnalyzeGenotype * found_mom; in FindSexLineage() 5648 cAnalyzeGenotype * genotype; in CommandMapDepth() 6009 cAnalyzeGenotype* new_genotype0 = new cAnalyzeGenotype(m_world, test_genome0); in CommandRecombine() 6010 cAnalyzeGenotype* new_genotype1 = new cAnalyzeGenotype(m_world, test_genome1); in CommandRecombine() 6109 cAnalyzeGenotype* new_genotype0 = new cAnalyzeGenotype(m_world, test_genome0); in CommandRecombineSample() 8496 cAnalyzeGenotype * new_genotype = new cAnalyzeGenotype(*genotype); in BatchDuplicate() [all …]
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H A D | cAnalyze.h | 47 class cAnalyzeGenotype; variable 160 cAnalyzeGenotype* PopGenotype(cString gen_desc, int batch_id = -1); 186 … tListIterator< tDataEntryCommand<cAnalyzeGenotype> >& output_it, int time_step = -1); 188 tListIterator< tDataEntryCommand<cAnalyzeGenotype> > & output_it, 191 tListIterator< tDataEntryCommand<cAnalyzeGenotype> >& output_it); 193 tListIterator< tDataEntryCommand<cAnalyzeGenotype> >& output_it); 195 tListIterator< tDataEntryCommand<cAnalyzeGenotype> >& output_it); 325 double AnalyzeEntropy(cAnalyzeGenotype* genotype, double mut_rate); 328 …double AnalyzeEntropyGivenParent(cAnalyzeGenotype* genotype, cAnalyzeGenotype* parent, double mut_… 333 double IncreasedInfo(cAnalyzeGenotype* genotype1, cAnalyzeGenotype* genotype2, double mut_rate); [all …]
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H A D | cAnalyzeTreeStats_CumulativeStemminess.h | 32 class cAnalyzeGenotype; variable 42 cAnalyzeGenotype *genotype; 95 void AnalyzeBatchTree(tList<cAnalyzeGenotype> &genotype_list);
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H A D | cAnalyzeTreeStats_CumulativeStemminess.cc | 78 void cAnalyzeTreeStats_CumulativeStemminess::AnalyzeBatchTree(tList<cAnalyzeGenotype> &genotype_lis… in AnalyzeBatchTree() 79 cAnalyzeGenotype * genotype = NULL; in AnalyzeBatchTree() 80 tListIterator<cAnalyzeGenotype> batch_it(genotype_list); in AnalyzeBatchTree() 96 tArray<cAnalyzeGenotype *> gen_array(num_gens); in AnalyzeBatchTree() 141 cAnalyzeGenotype * genotype = m_agl[pos].genotype; in AnalyzeBatchTree()
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/dports/biology/avida/avida-2.12.4-src/avida-core/source/script/ |
H A D | ASAvidaLib.cc | 46 tASNativeObject<cAnalyzeGenotype>::InitializeMethodRegistrar(); in setupNativeObjects() 47 REGISTER_C_METHOD(cAnalyzeGenotype, "Name", GetName, const cString& ()); in setupNativeObjects() 67 …REGISTER_C_METHOD(cGenotypeBatch, "FindGenotypeNumCPUs", FindGenotypeNumCPUs, cAnalyzeGenotype* ()… in setupNativeObjects() 68 REGISTER_S_METHOD(cGenotypeBatch, "PopGenotypeNumCPUs", PopGenotypeNumCPUs, cAnalyzeGenotype* ()); in setupNativeObjects() 73 …REGISTER_C_METHOD(cGenotypeBatch, "FindGenotypeFitness", FindGenotypeFitness, cAnalyzeGenotype* ()… in setupNativeObjects() 74 REGISTER_S_METHOD(cGenotypeBatch, "PopGenotypeFitness", PopGenotypeFitness, cAnalyzeGenotype* ()); in setupNativeObjects() 75 REGISTER_C_METHOD(cGenotypeBatch, "FindGenotypeID", FindGenotypeID, cAnalyzeGenotype* (int)); in setupNativeObjects() 76 REGISTER_S_METHOD(cGenotypeBatch, "PopGenotypeID", PopGenotypeID, cAnalyzeGenotype* (int)); in setupNativeObjects() 82 …REGISTER_C_METHOD(cGenotypeBatch, "FindLineage", FindLineage, cGenotypeBatch* (cAnalyzeGenotype*)); in setupNativeObjects() 84 REGISTER_C_METHOD(cGenotypeBatch, "FindClade", FindClade, cGenotypeBatch* (cAnalyzeGenotype*)); in setupNativeObjects() [all …]
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H A D | ASAnalyzeLib.cc | 58 cAnalyzeGenotype* genotype = new cAnalyzeGenotype(world, genome, *inst_set); in LoadOrganismWithInstSet() 71 cAnalyzeGenotype* LoadOrganism(cWorld* world, const cString& filename) in LoadOrganism() 81 return new cAnalyzeGenotype(world, seq, *inst_set); in LoadSequenceWithInstSet() 85 cAnalyzeGenotype* LoadSequence(cWorld* world, const cString& seq) in LoadSequence() 88 return new cAnalyzeGenotype(world, seq, world->GetHardwareManager().GetInstSet()); in LoadSequence() 115 tList< tDataEntryCommand<cAnalyzeGenotype> > output_list; in LoadBatchWithInstSet() 116 tListIterator< tDataEntryCommand<cAnalyzeGenotype> > output_it(output_list); in LoadBatchWithInstSet() 128 cAnalyzeGenotype* genotype = new cAnalyzeGenotype(world, default_genome, *inst_set); in LoadBatchWithInstSet() 131 tDataEntryCommand<cAnalyzeGenotype>* data_command = NULL; in LoadBatchWithInstSet() 175 BIND_FUNCTION(cWorld, "LoadOrganism", LoadOrganism, cAnalyzeGenotype* (const cString&)); in RegisterASAnalyzeLib() [all …]
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H A D | ASAvidaNativeObjects.h | 33 AS_DECLARE_NATIVE_OBJECT("Genotype", cAnalyzeGenotype);
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/dports/biology/avida/avida-2.12.4-src/avida-core/source/actions/ |
H A D | LandscapeActions.cc | 98 cAnalyzeGenotype* genotype = NULL; in Process() 258 cAnalyzeGenotype* genotype = NULL; in Process() 326 cAnalyzeGenotype* genotype = NULL; in Process() 411 cAnalyzeGenotype* genotype = NULL; in Process() 485 cAnalyzeGenotype* genotype = NULL; in Process() 551 cAnalyzeGenotype* genotype = NULL; in Process() 601 cAnalyzeGenotype* genotype = NULL; in Process() 659 cAnalyzeGenotype* genotype = NULL; in Process() 729 cAnalyzeGenotype* genotype = NULL; in Process() 790 cAnalyzeGenotype* genotype = NULL; in Process() [all …]
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H A D | PrintActions.cc | 2023 tListIterator<cAnalyzeGenotype> batch_it(m_world->GetAnalyze().GetCurrentBatch().List()); in Process() 2024 cAnalyzeGenotype* genotype = NULL; in Process() 2191 tListIterator<cAnalyzeGenotype> batch_it(m_world->GetAnalyze().GetCurrentBatch().List()); in Process() 2192 cAnalyzeGenotype* genotype = NULL; in Process() 2270 tListIterator<cAnalyzeGenotype> batch_it(m_world->GetAnalyze().GetCurrentBatch().List()); in Process() 2271 cAnalyzeGenotype* genotype = NULL; in Process() 2386 tListIterator<cAnalyzeGenotype> batch_it(m_world->GetAnalyze().GetCurrentBatch().List()); in Process() 2387 cAnalyzeGenotype* genotype = NULL; in Process()
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/dports/biology/avida/avida-2.12.4-src/avida-core/source/core/ |
H A D | Avida.cc | 54 cAnalyzeGenotype::Initialize(); in Initialize()
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/dports/biology/avida/avida-2.12.4-src/avida-core/source/main/ |
H A D | cWorld.h | 40 class cAnalyzeGenotype; variable
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/dports/biology/avida/avida-2.12.4-src/avida-core/source/ |
H A D | Jamfile | 27 analyze/cAnalyzeGenotype.cc
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/dports/biology/avida/avida-2.12.4-src/avida-core/Avida-Core.xcodeproj/ |
H A D | project.pbxproj | 70 …D0C0A431B00362B9C /* cAnalyzeGenotype.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70422A2409… 693 …A5E67F /* cAnalyzeGenotype.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType =… 694 …000A5E67F /* cAnalyzeGenotype.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType… 1366 70422A24091B141000A5E67F /* cAnalyzeGenotype.cc */, 1367 70422A25091B141000A5E67F /* cAnalyzeGenotype.h */, 2283 7023EC3D0C0A431B00362B9C /* cAnalyzeGenotype.cc in Sources */,
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