fixed bug with dist.shared subsampling. added mode parameter to dist.shared so...

[mothur.git] / indicatorcommand.cpp

diff --git a/indicatorcommand.cpp b/indicatorcommand.cpp
index fe99c46847ff08fa8359f6899a4ddf9a095126ea..8d1d7f7a6864b261a0a31611a1e02270730cfd32 100644 (file)
--- a/indicatorcommand.cpp
+++ b/indicatorcommand.cpp
@@ -99,7 +99,6 @@ IndicatorCommand::IndicatorCommand(string option)  {
                        m->clearGroups();
                        m->clearAllGroups();
                        m->Treenames.clear();
-                       m->names.clear();
                        
                        vector<string> tempOutNames;
                        outputTypes["tree"] = tempOutNames;
@@ -236,13 +235,11 @@ int IndicatorCommand::execute(){
                        designMap->readDesignMap();
                        
                        //fill Groups - checks for "all" and for any typo groups
-                       SharedUtil* util = new SharedUtil();
+                       SharedUtil util;
                        vector<string> nameGroups = designMap->getNamesOfGroups();
-                       util->setGroups(Groups, nameGroups);
+                       util.setGroups(Groups, nameGroups);
                        designMap->setNamesOfGroups(nameGroups);
-                       delete util;
                        
-                       //loop through the Groups and fill Globaldata's Groups with the design file info
                        vector<string> namesSeqs = designMap->getNamesSeqs(Groups);
                        m->setGroups(namesSeqs);
                }
@@ -320,8 +317,9 @@ int IndicatorCommand::execute(){
                                else { for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  } }
                                for (int i = 0; i < T.size(); i++) {  delete T[i];  }  delete treeMap; return 0; 
                        }
-                               
-                       T[0]->assembleTree();
+            
+                       map<string, string> nameMap;    
+                       T[0]->assembleTree(nameMap);
                                        
                        /***************************************************/
                        //    create ouptut tree - respecting pickedGroups //
@@ -329,7 +327,7 @@ int IndicatorCommand::execute(){
                        Tree* outputTree = new Tree(m->getNumGroups(), treeMap); 
                        
                        outputTree->getSubTree(T[0], m->getGroups());
-                       outputTree->assembleTree();
+                       outputTree->assembleTree(nameMap);
                                
                        //no longer need original tree, we have output tree to use and label
                        for (int i = 0; i < T.size(); i++) {  delete T[i];  } 
@@ -469,17 +467,17 @@ int IndicatorCommand::GetIndicatorSpecies(){
                                
                        if (m->control_pressed) { out.close(); return 0; }
                        
-                       out << (j+1) << '\t' << indicatorValues[j] << '\t'; 
+                       out << m->currentBinLabels[j] << '\t' << indicatorValues[j] << '\t'; 
                        
                        if (pValues[j] > (1/(float)iters)) { out << pValues[j] << endl; } 
                        else { out << "<" << (1/(float)iters) << endl; }
                        
                        if (pValues[j] <= 0.05) {
-                               cout << "OTU" << j+1 << '\t' << indicatorValues[j]  << '\t';
+                               cout << m->currentBinLabels[j] << '\t' << indicatorValues[j]  << '\t';
                                string pValueString = "<" + toString((1/(float)iters)); 
                                if (pValues[j] > (1/(float)iters)) { pValueString = toString(pValues[j]); cout << pValues[j];} 
                                else { cout << "<" << (1/(float)iters); }
-                               m->mothurOutJustToLog("OTU" + toString(j+1) + "\t" + toString(indicatorValues[j]) + "\t" + pValueString); 
+                               m->mothurOutJustToLog(m->currentBinLabels[j] + "\t" + toString(indicatorValues[j]) + "\t" + pValueString); 
                                m->mothurOutEndLine(); 
                        }
                }
@@ -515,7 +513,7 @@ int IndicatorCommand::GetIndicatorSpecies(Tree*& T){
                
                //print headings
                out << "TreeNode\t";
-               for (int i = 0; i < numBins; i++) { out << "OTU" << (i+1) << "_IndValue" << '\t' << "pValue" << '\t'; }
+               for (int i = 0; i < numBins; i++) { out << m->currentBinLabels[i] << "_IndValue" << '\t' << "pValue" << '\t'; }
                out << endl;
                
                m->mothurOutEndLine(); m->mothurOut("Node\tSpecies\tIndicatorValue\tpValue\n");
@@ -672,11 +670,11 @@ int IndicatorCommand::GetIndicatorSpecies(Tree*& T){
                                }
                                
                                if (pValues[j] <= 0.05) {
-                                       cout << i+1 << "\tOTU" << j+1 << '\t' << indicatorValues[j]  << '\t';
+                                       cout << i+1 << '\t' << m->currentBinLabels[j] << '\t' << indicatorValues[j]  << '\t';
                                        string pValueString = "<" + toString((1/(float)iters)); 
                                        if (pValues[j] > (1/(float)iters)) { pValueString = toString(pValues[j]); cout << pValues[j];} 
                                        else { cout << "<" << (1/(float)iters); }
-                                       m->mothurOutJustToLog(toString(i) + "\tOTU" + toString(j+1) + "\t" + toString(indicatorValues[j]) + "\t" + pValueString); 
+                                       m->mothurOutJustToLog(toString(i) + "\t" + m->currentBinLabels[j] + "\t" + toString(indicatorValues[j]) + "\t" + pValueString); 
                                        m->mothurOutEndLine(); 
                                }
                        }