X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcacommand.cpp;h=2cb37bda8896f8f2cb1f64521f1a73232507f24b;hb=8e67e9de1b200106bea5a468ac02125954656499;hp=3a92fa002559fcc7d7f19e1f5f91fe2574f4a3c1;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607;p=mothur.git

diff --git a/pcacommand.cpp b/pcacommand.cpp
index 3a92fa0..2cb37bd 100644
--- a/pcacommand.cpp
+++ b/pcacommand.cpp
@@ -48,6 +48,28 @@ string PCACommand::getHelpString(){
 		exit(1);
 	}
 }
+//**********************************************************************************************************************
+string PCACommand::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 == "pca") {  outputFileName =  "pca.axes"; }
+            else if (type == "loadings") {  outputFileName =  "pca.loadings"; }
+            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, "PCACommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+
 //**********************************************************************************************************************
 PCACommand::PCACommand(){	
 	try {
@@ -157,7 +179,7 @@ PCACommand::PCACommand(string option)  {
 			groups = validParameter.validFile(parameters, "groups", false);			
 			if (groups == "not found") { groups = "";  }
 			else { m->splitAtDash(groups, Groups);	}			
-			m->Groups = Groups;			
+			m->setGroups(Groups);			
 			
 		}
 		
@@ -365,7 +387,7 @@ int PCACommand::process(vector<SharedRAbundFloatVector*>& lookupFloat){
 		
 		string fbase = outputDir + m->getRootName(m->getSimpleName(inputFile));
 		string outputFileName = fbase + lookupFloat[0]->getLabel();
-		output(outputFileName, m->Groups, X, d);
+		output(outputFileName, m->getGroups(), X, d);
 		
 		if (metric) {   
 			
@@ -403,17 +425,19 @@ void PCACommand::output(string fnameRoot, vector<string> name_list, vector<vecto
 			dsum += d[i];
 		}
 		
-		ofstream pcaData((fnameRoot+".pca.axes").c_str(), ios::trunc);
+		ofstream pcaData;
+        m->openOutputFile((fnameRoot+"."+getOutputFileNameTag("pca")), pcaData);
 		pcaData.setf(ios::fixed, ios::floatfield);
 		pcaData.setf(ios::showpoint);	
-		outputNames.push_back(fnameRoot+".pca.axes");
-		outputTypes["pca"].push_back(fnameRoot+".pca.axes");
+		outputNames.push_back(fnameRoot+"."+getOutputFileNameTag("pca"));
+		outputTypes["pca"].push_back(fnameRoot+"."+getOutputFileNameTag("pca"));
 		
-		ofstream pcaLoadings((fnameRoot+".pca.loadings").c_str(), ios::trunc);
+		ofstream pcaLoadings;
+         m->openOutputFile((fnameRoot+"."+getOutputFileNameTag("loadings")), pcaLoadings);
 		pcaLoadings.setf(ios::fixed, ios::floatfield);
 		pcaLoadings.setf(ios::showpoint);
-		outputNames.push_back(fnameRoot+".pca.loadings");
-		outputTypes["loadings"].push_back(fnameRoot+".pca.loadings");	
+		outputNames.push_back(fnameRoot+"."+getOutputFileNameTag("loadings"));
+		outputTypes["loadings"].push_back(fnameRoot+"."+getOutputFileNameTag("loadings"));	
 		
 		pcaLoadings << "axis\tloading\n";
 		for(int i=0;i<numEigenValues;i++){