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

[mothur.git] / getrabundcommand.cpp

diff --git a/getrabundcommand.cpp b/getrabundcommand.cpp
index 5a33253ff1ec2b67a9e995b940f09349241494f5..5f33f3a1fbab70aad5764b20f4e1d8633c8a865b 100644 (file)
--- a/getrabundcommand.cpp
+++ b/getrabundcommand.cpp
@@ -47,7 +47,26 @@ string GetRAbundCommand::getHelpString(){
                exit(1);
        }
 }
-
+//**********************************************************************************************************************
+string GetRAbundCommand::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 == "rabund")            {   outputFileName = "rabund";  }
+            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, "GetRAbundCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 GetRAbundCommand::GetRAbundCommand(){  
        try {
@@ -173,7 +192,7 @@ int GetRAbundCommand::execute(){
        
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
-               filename = outputDir + m->getRootName(m->getSimpleName(inputfile)) + "rabund";
+               filename = outputDir + m->getRootName(m->getSimpleName(inputfile)) + getOutputFileNameTag("rabund");
                m->openOutputFile(filename, out);
                
                input = new InputData(inputfile, format);