X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=corraxescommand.cpp;h=c4454a5181c719302011e6e98410408826183735;hb=006601d68abe8d0061f77e8d28323b160750e343;hp=c27eb4b9ac335112f19244c708cee9bb8630feda;hpb=e41b86a600fe30f5df9507d7e55027e7b8bd7dd6;p=mothur.git

diff --git a/corraxescommand.cpp b/corraxescommand.cpp
index c27eb4b..c4454a5 100644
--- 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();