added count parameter to chimera.slayer command

[mothur.git] / indicatorcommand.cpp

diff --git a/indicatorcommand.cpp b/indicatorcommand.cpp
index 94d5c84344f86eb4676f0e71111e898c5c28596d..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 {
@@ -240,7 +260,6 @@ int IndicatorCommand::execute(){
                        util.setGroups(Groups, nameGroups);
                        designMap->setNamesOfGroups(nameGroups);
                        
-                       //loop through the Groups and fill Globaldata's Groups with the design file info
                        vector<string> namesSeqs = designMap->getNamesSeqs(Groups);
                        m->setGroups(namesSeqs);
                }
@@ -386,7 +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;
@@ -468,17 +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(); 
                        }
                }
@@ -501,7 +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;
@@ -514,14 +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
@@ -671,11 +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(); 
                                }
                        }