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Searched refs:cAnalyzeGenotype (Results 1 – 21 of 21) sorted by relevance

/dports/biology/avida/avida-2.12.4-src/avida-core/source/analyze/
H A DcGenotypeBatch.cc42 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()
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H A DcGenotypeBatch.h35 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);
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H A DcAnalyzeGenotype.cc52 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()
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H A DcModularityAnalysis.h36 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);
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H A DcAnalyzeTreeStats_Gamma.h34 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,
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H A DcAnalyzeGenotype.h76 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
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H A DcAnalyzeTreeStats_Gamma.cc37 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()
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H A DcModularityAnalysis.cc33 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()
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H A DcAnalyze.cc190 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()
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H A DcAnalyze.h47 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);
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H A DcAnalyzeTreeStats_CumulativeStemminess.h32 class cAnalyzeGenotype; variable
42 cAnalyzeGenotype *genotype;
95 void AnalyzeBatchTree(tList<cAnalyzeGenotype> &genotype_list);
H A DcAnalyzeTreeStats_CumulativeStemminess.cc78 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()
/dports/biology/avida/avida-2.12.4-src/avida-core/source/script/
H A DASAvidaLib.cc46 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()
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H A DASAnalyzeLib.cc58 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()
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H A DASAvidaNativeObjects.h33 AS_DECLARE_NATIVE_OBJECT("Genotype", cAnalyzeGenotype);
/dports/biology/avida/avida-2.12.4-src/avida-core/source/actions/
H A DLandscapeActions.cc98 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()
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H A DPrintActions.cc2023 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()
/dports/biology/avida/avida-2.12.4-src/avida-core/source/core/
H A DAvida.cc54 cAnalyzeGenotype::Initialize(); in Initialize()
/dports/biology/avida/avida-2.12.4-src/avida-core/source/main/
H A DcWorld.h40 class cAnalyzeGenotype; variable
/dports/biology/avida/avida-2.12.4-src/avida-core/source/
H A DJamfile27 analyze/cAnalyzeGenotype.cc
/dports/biology/avida/avida-2.12.4-src/avida-core/Avida-Core.xcodeproj/
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