added count parameter to chimera.slayer command

[mothur.git] / pcacommand.cpp

diff --git a/pcacommand.cpp b/pcacommand.cpp
index 3a92fa002559fcc7d7f19e1f5f91fe2574f4a3c1..2cb37bda8896f8f2cb1f64521f1a73232507f24b 100644 (file)
--- 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++){