X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=corraxescommand.cpp;h=f8083cc01c10a23b4626c6ea2ccd285a15f59c87;hb=49d2b7459c5027557564b21e9487dadafbbbdc96;hp=a1c3a3d6cd9e6849fb5f86be42a1d46bcd9bc138;hpb=5d77fd07180d1fb8561ff1962e6d7429caf8555e;p=mothur.git

diff --git a/corraxescommand.cpp b/corraxescommand.cpp
index a1c3a3d..f8083cc 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);
@@ -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