sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / pcoacommand.cpp

diff --git a/pcoacommand.cpp b/pcoacommand.cpp
index 02e165e978dc071ba19808139060866d7e41388c..2043a128bd94bc755cb7ef10f5a8b8d9bdb5a6be 100644 (file)
--- a/pcoacommand.cpp
+++ b/pcoacommand.cpp
@@ -15,10 +15,10 @@
 //**********************************************************************************************************************
 vector<string> PCOACommand::setParameters(){   
        try {
-               CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip);
-               CommandParameter pmetric("metric", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pmetric);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","pcoa-loadings",false,true,true); parameters.push_back(pphylip);
+               CommandParameter pmetric("metric", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pmetric);
+               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);          }
@@ -45,6 +45,22 @@ string PCOACommand::getHelpString(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+string PCOACommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "pcoa") {  pattern = "[filename],pcoa.axes"; } 
+        else if (type == "loadings") {  pattern = "[filename],pcoa.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, "PCOACommand", "getOutputPattern");
+        exit(1);
+    }
+}
 
 
 //**********************************************************************************************************************
@@ -229,17 +245,23 @@ void PCOACommand::output(string fnameRoot, vector<string> name_list, vector<vect
                        }
                }
                
-               ofstream pcaData((fnameRoot+"pcoa.axes").c_str(), ios::trunc);
+               ofstream pcaData;
+        map<string, string> variables; 
+        variables["[filename]"] = fnameRoot;
+        string pcoaDataFile = getOutputFileName("pcoa",variables);
+        m->openOutputFile(pcoaDataFile, pcaData);
                pcaData.setf(ios::fixed, ios::floatfield);
                pcaData.setf(ios::showpoint);   
-               outputNames.push_back(fnameRoot+"pcoa.axes");
-               outputTypes["pcoa"].push_back(fnameRoot+"pcoa.axes");
+               outputNames.push_back(pcoaDataFile);
+               outputTypes["pcoa"].push_back(pcoaDataFile);
                
-               ofstream pcaLoadings((fnameRoot+"pcoa.loadings").c_str(), ios::trunc);
+               ofstream pcaLoadings;
+        string loadingsFile = getOutputFileName("loadings",variables);
+        m->openOutputFile(loadingsFile, pcaLoadings);
                pcaLoadings.setf(ios::fixed, ios::floatfield);
                pcaLoadings.setf(ios::showpoint);
-               outputNames.push_back(fnameRoot+"pcoa.loadings");
-               outputTypes["loadings"].push_back(fnameRoot+"pcoa.loadings");   
+               outputNames.push_back(loadingsFile);
+               outputTypes["loadings"].push_back(loadingsFile);        
                
                pcaLoadings << "axis\tloading\n";
                for(int i=0;i<rank;i++){