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

[mothur.git] / degapseqscommand.cpp

diff --git a/degapseqscommand.cpp b/degapseqscommand.cpp
index 1d83f3bef00d08574a66d7e5ecf21efa148452a4..318a05ec0bee7765f835cce4301d2b7a97d16978 100644 (file)
--- a/degapseqscommand.cpp
+++ b/degapseqscommand.cpp
@@ -46,6 +46,26 @@ string DegapSeqsCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string DegapSeqsCommand::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 == "fasta") {  outputFileName =  "ng.fasta"; }
+            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, "DegapSeqsCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 DegapSeqsCommand::DegapSeqsCommand(){  
        try {
                abort = true; calledHelp = true; 
@@ -193,7 +213,7 @@ int DegapSeqsCommand::execute(){
                        ofstream outFASTA;
                        string tempOutputDir = outputDir;
                        if (outputDir == "") { tempOutputDir = m->hasPath(fastaFileNames[s]); }
-                       string degapFile = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "ng.fasta";
+                       string degapFile = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("fasta");
                        m->openOutputFile(degapFile, outFASTA);
                        
                        while(!inFASTA.eof()){