Merge remote-tracking branch 'origin/master'

[mothur.git] / corraxescommand.cpp

diff --git a/corraxescommand.cpp b/corraxescommand.cpp
index c27eb4b9ac335112f19244c708cee9bb8630feda..c4454a5181c719302011e6e98410408826183735 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);
@@ -905,16 +925,11 @@ int CorrAxesCommand::getMetadata(){
                m->openInputFile(metadatafile, in);
                
                string headerLine = m->getline(in); m->gobble(in);
-               istringstream iss (headerLine,istringstream::in);
-               
-               //read the first label, because it refers to the groups
-               string columnLabel;
-               iss >> columnLabel; m->gobble(iss); 
+               vector<string> pieces = m->splitWhiteSpace(headerLine);
                
                //save names of columns you are reading
-               while (!iss.eof()) {
-                       iss >> columnLabel; m->gobble(iss);
-                       metadataLabels.push_back(columnLabel);
+               for (int i = 1; i < pieces.size(); i++) {
+                       metadataLabels.push_back(pieces[i]);
                }
                int count = metadataLabels.size();