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

[mothur.git] / nmdscommand.cpp

diff --git a/nmdscommand.cpp b/nmdscommand.cpp
index e2a3712a410738b0396884accc41bdd555caa735..900f50bd43ffb2aaee98f279023e684bb8d7c00d 100644 (file)
--- a/nmdscommand.cpp
+++ b/nmdscommand.cpp
@@ -55,6 +55,28 @@ string NMDSCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string NMDSCommand::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 == "nmds") {  outputFileName =  "nmds.axes"; }
+            else if (type == "stress") {  outputFileName =  "nmds.stress"; }
+            else if (type == "iters") {  outputFileName =  "nmds.iters"; }
+            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, "NMDSCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 NMDSCommand::NMDSCommand(){    
        try {
                abort = true; calledHelp = true; 
@@ -186,8 +208,8 @@ int NMDSCommand::execute(){
                vector< vector<double> > axes;
                if (axesfile != "") {  axes = readAxes(names);          }
                
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "nmds.iters";
-               string stressFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "nmds.stress";
+               string outputFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + getOutputFileNameTag("iters");
+               string stressFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + getOutputFileNameTag("stress");
                outputNames.push_back(outputFileName); outputTypes["iters"].push_back(outputFileName);
                outputNames.push_back(stressFileName); outputTypes["stress"].push_back(stressFileName);
                
@@ -256,7 +278,7 @@ int NMDSCommand::execute(){
                out.close(); out2.close();
                
                //output best config
-               string BestFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "nmds.axes";
+               string BestFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + getOutputFileNameTag("nmds");
                outputNames.push_back(BestFileName); outputTypes["nmds"].push_back(BestFileName);
                
                m->mothurOut("\nNumber of dimensions:\t" + toString(bestDim) + "\n");