[Avida-SVN] r2934 - in development/source: analyze script

[brysonda at myxo.css.msu.edu]

Author: brysonda
Date: 2008-11-11 13:00:40 -0500 (Tue, 11 Nov 2008)
New Revision: 2934

Modified:
   development/source/analyze/cGenotypeBatch.cc
   development/source/analyze/cGenotypeBatch.h
   development/source/script/ASAvidaLib.cc
Log:
Implement cGenotypeBatch::FindLastCommonAncestor.

Modified: development/source/analyze/cGenotypeBatch.cc
===================================================================
--- development/source/analyze/cGenotypeBatch.cc	2008-11-11 16:36:51 UTC (rev 2933)
+++ development/source/analyze/cGenotypeBatch.cc	2008-11-11 18:00:40 UTC (rev 2934)
@@ -145,6 +145,50 @@
 }
 
 
+cAnalyzeGenotype* cGenotypeBatch::FindLastCommonAncestor()
+{
+  // Assumes that the batch contains a population and all of its common ancestors
+  // Finds the last common ancestor among all current organisms that are still alive,
+  // i.e. have an update_died of -1.
+  
+  // Connect each genotype to its parent.
+  tListIterator<cAnalyzeGenotype> it(m_list);
+  tListIterator<cAnalyzeGenotype> parent_it(m_list);
+  cAnalyzeGenotype* on_child = NULL;
+  while ((on_child = it.Next())) {
+    parent_it.Reset();
+    cAnalyzeGenotype* on_parent = NULL;
+    while ((on_parent = parent_it.Next())) {
+      if (on_child->GetParentID() == on_parent->GetID()) {
+        on_child->LinkParent(on_parent);
+        break;
+      }
+    }
+  }
+    
+  // Find the genotype without a parent (there should only be one)
+  it.Reset();
+  cAnalyzeGenotype* lca = NULL;
+  cAnalyzeGenotype* test_lca = NULL;
+  while ((test_lca = it.Next())) {
+    if (!test_lca->GetParent()) {
+      // It is an error to get two genotypes without a parent
+      if (lca) return NULL;
+      lca = test_lca;
+    }
+  }
+  
+  // Follow the children from this parent until we find a genotype with more than one child.
+  // This is the last common ancestor.
+  while (lca->GetChildList().GetSize() == 1) {
+    lca = lca->GetChildList().Pop();
+  }
+  
+  return new cAnalyzeGenotype(*lca);
+}
+
+
+
 cGenotypeBatch* cGenotypeBatch::FindLineage(cAnalyzeGenotype* end_genotype) const
 {
   if ((end_genotype)) return FindLineage(end_genotype->GetID());

Modified: development/source/analyze/cGenotypeBatch.h
===================================================================
--- development/source/analyze/cGenotypeBatch.h	2008-11-11 16:36:51 UTC (rev 2933)
+++ development/source/analyze/cGenotypeBatch.h	2008-11-11 18:00:40 UTC (rev 2934)
@@ -89,6 +89,8 @@
   inline cAnalyzeGenotype* FindOrganismRandom(cRandom* rng) const { return FindOrganismRandom(*rng); }
   inline cAnalyzeGenotype* PopOrganismRandom(cRandom* rng) { return PopOrganismRandom(*rng); }
   
+  cAnalyzeGenotype* FindLastCommonAncestor();
+  
   cGenotypeBatch* FindLineage(cAnalyzeGenotype* end_genotype) const;
   cGenotypeBatch* FindLineage(int end_genotype_id) const;
 

Modified: development/source/script/ASAvidaLib.cc
===================================================================
--- development/source/script/ASAvidaLib.cc	2008-11-11 16:36:51 UTC (rev 2933)
+++ development/source/script/ASAvidaLib.cc	2008-11-11 18:00:40 UTC (rev 2934)
@@ -81,6 +81,7 @@
 //  REGISTER_S_METHOD(cGenotypeBatch, "PopGenotypeRandom", PopGenotypeRandom, cAnalyzeGenotype* (cRandom*));
 //  REGISTER_C_METHOD(cGenotypeBatch, "FindOrganismRandom", FindOrganismRandom, cAnalyzeGenotype* (cRandom*));
 //  REGISTER_S_METHOD(cGenotypeBatch, "PopOrganismRandom", PopOrganismRandom, cAnalyzeGenotype* (cRandom*));
+  REGISTER_S_METHOD(cGenotypeBatch, "FindLastCommonAncestor", FindLastCommonAncestor, cAnalyzeGenotype* ());
   REGISTER_C_METHOD(cGenotypeBatch, "FindLineage", FindLineage, cGenotypeBatch* (cAnalyzeGenotype*));
   REGISTER_C_METHOD(cGenotypeBatch, "FindSexLineage", FindSexLineage, cGenotypeBatch* (cAnalyzeGenotype*, bool));
   REGISTER_C_METHOD(cGenotypeBatch, "FindClade", FindClade, cGenotypeBatch* (cAnalyzeGenotype*));