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

[mothur.git] / deuniqueseqscommand.cpp

diff --git a/deuniqueseqscommand.cpp b/deuniqueseqscommand.cpp
index 7481416f649ddad983877ab02cac08e5668316d1..918079cfe45aa2fbe6f14b155a6edd494e555c1d 100644 (file)
--- a/deuniqueseqscommand.cpp
+++ b/deuniqueseqscommand.cpp
@@ -45,6 +45,26 @@ string DeUniqueSeqsCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string DeUniqueSeqsCommand::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 =  "redundant.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, "DeUniqueSeqsCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 DeUniqueSeqsCommand::DeUniqueSeqsCommand(){    
        try {
                abort = true; calledHelp = true; 
@@ -148,9 +168,9 @@ int DeUniqueSeqsCommand::execute() {
                string outFastaFile = m->getRootName(m->getSimpleName(fastaFile));
                int pos = outFastaFile.find("unique");
                if (pos != string::npos) {
-                       outFastaFile = outputDir + outFastaFile.substr(0, pos) + "redundant" + m->getExtension(fastaFile);
+                       outFastaFile = outputDir + outFastaFile.substr(0, pos) + getOutputFileNameTag("fasta");
                }else{
-                       outFastaFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "redundant" + m->getExtension(fastaFile);
+                       outFastaFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + getOutputFileNameTag("fasta");
                }
                m->openOutputFile(outFastaFile, out);