working on mgcluster count file change

[mothur.git] / listseqscommand.cpp

diff --git a/listseqscommand.cpp b/listseqscommand.cpp
index 833ac952a8db761b16ba59d9b53b561bef07ad0b..bfbb0788c5092382f22bea643c5405674361dd67 100644 (file)
--- a/listseqscommand.cpp
+++ b/listseqscommand.cpp
@@ -49,7 +49,26 @@ string ListSeqsCommand::getHelpString(){
                exit(1);
        }
 }
-
+//**********************************************************************************************************************
+string ListSeqsCommand::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 == "accnos")             {   outputFileName =  "accnos";       }
+            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, "ListSeqsCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 ListSeqsCommand::ListSeqsCommand(){    
        try {
@@ -214,7 +233,7 @@ int ListSeqsCommand::execute(){
                
                if (outputDir == "") {  outputDir += m->hasPath(inputFileName);  }
                
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + "accnos";
+               string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + getOutputFileNameTag("accnos");
 
                ofstream out;
                m->openOutputFile(outputFileName, out);
@@ -400,14 +419,14 @@ int ListSeqsCommand::readAlign(){
                        if (!in.eof())  {       in >> junk;             }
                        else                    {       break;                  }
                }
-               
+               //m->getline(in);
                
                while(!in.eof()){
                
                        if (m->control_pressed) { in.close(); return 0; }
 
                        in >> name;                             //read from first column
-                       
+                       //m->getline(in);
                        //read rest
                        for (int i = 0; i < 15; i++) {  
                                if (!in.eof())  {       in >> junk;             }