added load.logfile command. changed summary.single output for subsample=t.

[mothur.git] / indicatorcommand.cpp

diff --git a/indicatorcommand.cpp b/indicatorcommand.cpp
index 1864f7473b0e21ff06d84ce76968f81374189954..f98620b2ee0bd4cc70bc10d1db908d8de40de995 100644 (file)
--- a/indicatorcommand.cpp
+++ b/indicatorcommand.cpp
@@ -57,7 +57,27 @@ string IndicatorCommand::getHelpString(){
                exit(1);
        }
 }
-
+//**********************************************************************************************************************
+string IndicatorCommand::getOutputFileNameTag(string type, string inputName=""){       
+       try {
+        string outputFileName = "";
+               map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "tree")       {   outputFileName =  "indicator.tre";   }
+            else if (type == "summary")    {   outputFileName =  "indicator.summary";   }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "IndicatorCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 IndicatorCommand::IndicatorCommand(){  
        try {
@@ -99,7 +119,6 @@ IndicatorCommand::IndicatorCommand(string option)  {
                        m->clearGroups();
                        m->clearAllGroups();
                        m->Treenames.clear();
-                       m->names.clear();
                        
                        vector<string> tempOutNames;
                        outputTypes["tree"] = tempOutNames;
@@ -236,13 +255,11 @@ 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 +337,9 @@ 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 //
@@ -329,12 +347,11 @@ 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];  } 
                        
-                                       
                        if (m->control_pressed) { 
                                if (designfile != "") { delete designMap; }
                                if (sharedfile != "") {  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } }
@@ -388,7 +405,7 @@ int IndicatorCommand::GetIndicatorSpecies(){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(inputFileName);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + "indicator.summary";
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + getOutputFileNameTag("summary");
                outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
                
                ofstream out;
@@ -470,17 +487,17 @@ 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(); 
                        }
                }
@@ -503,7 +520,7 @@ int IndicatorCommand::GetIndicatorSpecies(Tree*& T){
                
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(inputFileName);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + "indicator.summary";
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + getOutputFileNameTag("summary");
                outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
                
                ofstream out;
@@ -516,14 +533,14 @@ 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");
                
                string treeOutputDir = outputDir;
                if (outputDir == "") {  treeOutputDir += m->hasPath(treefile);  }
-               string outputTreeFileName = treeOutputDir + m->getRootName(m->getSimpleName(treefile)) + "indicator.tre";
+               string outputTreeFileName = treeOutputDir + m->getRootName(m->getSimpleName(treefile)) + getOutputFileNameTag("tree");
                
                
                //create a map from tree node index to names of descendants, save time later to know which sharedRabund you need
@@ -673,11 +690,11 @@ 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(); 
                                }
                        }
@@ -1120,7 +1137,7 @@ vector<float> IndicatorCommand::getPValues(vector< vector<SharedRAbundFloatVecto
        try {
                vector<float> pvalues;
                
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                if(processors == 1){
                        pvalues = driver(groupings, groupingsMap, num, indicatorValues, iters);
                        for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; }
@@ -1234,7 +1251,7 @@ vector<float> IndicatorCommand::getPValues(vector< vector<SharedRAbundVector*> >
        try {
                vector<float> pvalues;
                
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                if(processors == 1){
                        pvalues = driver(groupings, groupingsMap, num, indicatorValues, iters);
                        for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; }