sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / pcacommand.cpp

diff --git a/pcacommand.cpp b/pcacommand.cpp
index 2cb37bda8896f8f2cb1f64521f1a73232507f24b..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);          }
@@ -49,25 +49,20 @@ string PCACommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
-string PCACommand::getOutputFileNameTag(string type, string inputName=""){     
-       try {
-        string outputFileName = "";
-               map<string, vector<string> >::iterator it;
+string PCACommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
         
-        //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);
-       }
+        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);
+    }
 }
 
 //**********************************************************************************************************************
@@ -386,8 +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->getGroups(), X, d);
+               //string outputFileName = fbase + lookupFloat[0]->getLabel();
+               output(fbase, lookupFloat[0]->getLabel(), m->getGroups(), X, d);
                
                if (metric) {   
                        
@@ -416,7 +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();
@@ -426,18 +421,23 @@ void PCACommand::output(string fnameRoot, vector<string> name_list, vector<vecto
                }
                
                ofstream pcaData;
-        m->openOutputFile((fnameRoot+"."+getOutputFileNameTag("pca")), 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+"."+getOutputFileNameTag("pca"));
-               outputTypes["pca"].push_back(fnameRoot+"."+getOutputFileNameTag("pca"));
+               outputNames.push_back(pcaFileName);
+               outputTypes["pca"].push_back(pcaFileName);
                
                ofstream pcaLoadings;
-         m->openOutputFile((fnameRoot+"."+getOutputFileNameTag("loadings")), pcaLoadings);
+        string loadingsFilename = getOutputFileName("loadings",variables);
+         m->openOutputFile(loadingsFilename, pcaLoadings);
                pcaLoadings.setf(ios::fixed, ios::floatfield);
                pcaLoadings.setf(ios::showpoint);
-               outputNames.push_back(fnameRoot+"."+getOutputFileNameTag("loadings"));
-               outputTypes["loadings"].push_back(fnameRoot+"."+getOutputFileNameTag("loadings"));      
+               outputNames.push_back(loadingsFilename);
+               outputTypes["loadings"].push_back(loadingsFilename);    
                
                pcaLoadings << "axis\tloading\n";
                for(int i=0;i<numEigenValues;i++){