changes while testing 1.27

[mothur.git] / corraxescommand.cpp

diff --git a/corraxescommand.cpp b/corraxescommand.cpp
index a1c3a3d6cd9e6849fb5f86be42a1d46bcd9bc138..f8083cc01c10a23b4626c6ea2ccd285a15f59c87 100644 (file)
--- a/corraxescommand.cpp
+++ b/corraxescommand.cpp
@@ -56,12 +56,32 @@ string CorrAxesCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string CorrAxesCommand::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 == "corraxes") {  outputFileName =  "corr.axes"; }
+            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, "CorrAxesCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 CorrAxesCommand::CorrAxesCommand(){    
        try {
                abort = true; calledHelp = true; 
                setParameters();
                vector<string> tempOutNames;
-               outputTypes["corr.axes"] = tempOutNames;
+               outputTypes["corraxes"] = tempOutNames;
        }
        catch(exception& e) {
                m->errorOut(e, "CorrAxesCommand", "CorrAxesCommand");
@@ -92,7 +112,7 @@ CorrAxesCommand::CorrAxesCommand(string option)  {
                        }
                        
                        vector<string> tempOutNames;
-                       outputTypes["corr.axes"] = tempOutNames;
+                       outputTypes["corraxes"] = tempOutNames;
                        
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
                        string inputDir = validParameter.validFile(parameters, "inputdir", false);              
@@ -266,8 +286,8 @@ int CorrAxesCommand::execute(){
                // calc the r values                                                                                                                            //
                /************************************************************************************/
                
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + method + ".corr.axes";
-               outputNames.push_back(outputFileName); outputTypes["corr.axes"].push_back(outputFileName);      
+               string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + method + "." + getOutputFileNameTag("corraxes");
+               outputNames.push_back(outputFileName); outputTypes["corraxes"].push_back(outputFileName);       
                ofstream out;
                m->openOutputFile(outputFileName, out);
                out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
@@ -321,7 +341,7 @@ int CorrAxesCommand::calcPearson(map<string, vector<float> >& axes, ofstream& ou
           //for each otu
           for (int i = 0; i < lookupFloat[0]->getNumBins(); i++) {
                   
-                  if (metadatafile == "") {  out << i+1;       }
+                  if (metadatafile == "") {  out << m->currentBinLabels[i];    }
                   else {  out << metadataLabels[i];            }
                                   
                   //find the averages this otu - Y
@@ -456,7 +476,7 @@ int CorrAxesCommand::calcSpearman(map<string, vector<float> >& axes, ofstream& o
                //for each otu
                for (int i = 0; i < lookupFloat[0]->getNumBins(); i++) {
                        
-                       if (metadatafile == "") {  out << i+1;  }
+                       if (metadatafile == "") {  out << m->currentBinLabels[i];       }
                        else {  out << metadataLabels[i];               }
                        
                        //find the ranks of this otu - Y
@@ -609,7 +629,7 @@ int CorrAxesCommand::calcKendall(map<string, vector<float> >& axes, ofstream& ou
                //for each otu
                for (int i = 0; i < lookupFloat[0]->getNumBins(); i++) {
                
-                       if (metadatafile == "") {  out << i+1;  }
+                       if (metadatafile == "") {  out << m->currentBinLabels[i];       }
                        else {  out << metadataLabels[i];               }
                        
                        //find the ranks of this otu - Y