sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / pcacommand.cpp

diff --git a/pcacommand.cpp b/pcacommand.cpp
index 3a92fa002559fcc7d7f19e1f5f91fe2574f4a3c1..7103adb8a150a3e6f9871989ba94bd45d2b6a542 100644 (file)
--- a/pcacommand.cpp
+++ b/pcacommand.cpp
@@ -13,13 +13,13 @@
 //**********************************************************************************************************************
 vector<string> PCACommand::setParameters(){    
        try {
-               CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);    
-               CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prelabund);
-               CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
-               CommandParameter pmetric("metric", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pmetric);
-               CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","pca-loadings",false,false,true); parameters.push_back(pshared);        
+               CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none","pca-loadings",false,false,true); parameters.push_back(prelabund);
+               CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+               CommandParameter pmetric("metric", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pmetric);
+               CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -48,6 +48,23 @@ string PCACommand::getHelpString(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+string PCACommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "pca") {  pattern = "[filename],[distance],pca.axes"; } 
+        else if (type == "loadings") {  pattern = "[filename],[distance],pca.loadings"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "PCACommand", "getOutputPattern");
+        exit(1);
+    }
+}
+
 //**********************************************************************************************************************
 PCACommand::PCACommand(){      
        try {
@@ -157,7 +174,7 @@ 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);                   
                        
                }
                
@@ -364,8 +381,8 @@ int PCACommand::process(vector<SharedRAbundFloatVector*>& lookupFloat){
                if (m->control_pressed) { return 0; }
                
                string fbase = outputDir + m->getRootName(m->getSimpleName(inputFile));
-               string outputFileName = fbase + lookupFloat[0]->getLabel();
-               output(outputFileName, m->Groups, X, d);
+               //string outputFileName = fbase + lookupFloat[0]->getLabel();
+               output(fbase, lookupFloat[0]->getLabel(), m->getGroups(), X, d);
                
                if (metric) {   
                        
@@ -394,7 +411,7 @@ int PCACommand::process(vector<SharedRAbundFloatVector*>& lookupFloat){
 }
 /*********************************************************************************************************************************/
 
-void PCACommand::output(string fnameRoot, vector<string> name_list, vector<vector<double> >& G, vector<double> d) {
+void PCACommand::output(string fbase, string label, vector<string> name_list, vector<vector<double> >& G, vector<double> d) {
        try {
 
                int numEigenValues = d.size();
@@ -403,17 +420,24 @@ 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;
+        map<string, string> variables; 
+        variables["[filename]"] = fbase;
+        variables["[distance]"] = label;
+        string pcaFileName = getOutputFileName("pca",variables);
+        m->openOutputFile(pcaFileName, 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(pcaFileName);
+               outputTypes["pca"].push_back(pcaFileName);
                
-               ofstream pcaLoadings((fnameRoot+".pca.loadings").c_str(), ios::trunc);
+               ofstream pcaLoadings;
+        string loadingsFilename = getOutputFileName("loadings",variables);
+         m->openOutputFile(loadingsFilename, 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(loadingsFilename);
+               outputTypes["loadings"].push_back(loadingsFilename);    
                
                pcaLoadings << "axis\tloading\n";
                for(int i=0;i<numEigenValues;i++){