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

[mothur.git] / shhhseqscommand.cpp

diff --git a/shhhseqscommand.cpp b/shhhseqscommand.cpp
index 5c6359ec58bb776ce9a050a132e8409e60cf197b..63de2bb5541ddbd653b90eced12b4d59a9084629 100644 (file)
--- a/shhhseqscommand.cpp
+++ b/shhhseqscommand.cpp
@@ -54,6 +54,29 @@ string ShhhSeqsCommand::getHelpString(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+string ShhhSeqsCommand::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 =  "shhh_seqs.fasta";   }
+            else if (type == "name")    {   outputFileName =  "shhh_seqs.names";   }
+            else if (type == "map")        {   outputFileName =  "shhh_seqs.map";   }
+            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, "ShhhSeqsCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+
 //**********************************************************************************************************************
 
 ShhhSeqsCommand::ShhhSeqsCommand(){    
@@ -185,9 +208,9 @@ int ShhhSeqsCommand::execute() {
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                if (outputDir == "") { outputDir = m->hasPath(fastafile);  }//if user entered a file with a path then preserve it                               
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "shhh.fasta";
-               string nameFileName = outputDir + m->getRootName(m->getSimpleName(fastafile))  + "shhh.names";
-               string mapFileName = outputDir + m->getRootName(m->getSimpleName(fastafile))  + "shhh.map";
+               string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta");
+               string nameFileName = outputDir + m->getRootName(m->getSimpleName(fastafile))  + getOutputFileNameTag("name");
+               string mapFileName = outputDir + m->getRootName(m->getSimpleName(fastafile))  + getOutputFileNameTag("map");
                
                if (groupfile != "") {
                        //Parse sequences by group