Merge branch 'simulations' of https://github.com/raphael-group/machina into simulations

Author: melkebir

src/basetree.cpp

@@ -137,6 +137,12 @@ bool BaseTree::read(std::istream& in)
     }
   }
 
+  if (_idToNode.empty())
+  {
+    std::cerr << "Error: empty tree" << std::endl;
+    return false;
+  }
+  
   init();
 
   if (!isValid())

src/msenumeration.cpp

@@ -199,6 +199,16 @@ void MSEnumeration::run(const MigrationTree& migrationTree,
       }
       outFile.close();
 
+      snprintf(buf, 1024, "%s/T%s%d.tree", _outputDirectory.c_str(), migrationTreeString.c_str(), i);
+      std::ofstream outT(buf);
+      entry->_T.write(outT);
+      outT.close();
+      
+      snprintf(buf, 1024, "%s/T%s%d.labeling", _outputDirectory.c_str(), migrationTreeString.c_str(), i);
+      std::ofstream outLabeling(buf);
+      entry->_T.writeVertexLabeling(outT, entry->_lPlus);
+      outLabeling.close();
+      
 //      snprintf(buf, 1024, "%s/phyloT%s%d.dot", _outputDirectory.c_str(), migrationTreeString.c_str(), i);
 //      std::ofstream outFileT(buf);
 //      gm::PerfectPhyloTree phyloT(solutions.solution(i).A(), solutions.solution(i).S());