added load.logfile command. changed summary.single output for subsample=t.

[mothur.git] / pcoacommand.cpp

diff --git a/pcoacommand.cpp b/pcoacommand.cpp
index 02e165e978dc071ba19808139060866d7e41388c..354826f8c0b27a359b1eb1530e6a0d7a9fbaf32f 100644 (file)
--- a/pcoacommand.cpp
+++ b/pcoacommand.cpp
@@ -46,6 +46,27 @@ string PCOACommand::getHelpString(){
        }
 }
 
+//**********************************************************************************************************************
+string PCOACommand::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 == "pcoa") {  outputFileName =  "pcoa.axes"; }
+            else if (type == "loadings") {  outputFileName =  "pcoa.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, "PCOACommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 
 //**********************************************************************************************************************
 PCOACommand::PCOACommand(){    
@@ -229,17 +250,21 @@ void PCOACommand::output(string fnameRoot, vector<string> name_list, vector<vect
                        }
                }
                
-               ofstream pcaData((fnameRoot+"pcoa.axes").c_str(), ios::trunc);
+               ofstream pcaData;
+        string pcoaDataFile = fnameRoot+getOutputFileNameTag("pcoa");
+        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 = fnameRoot+getOutputFileNameTag("loadings");
+        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++){