X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayercommand.cpp;fp=chimeraslayercommand.cpp;h=59dd0a55a27c13eb80dd521ea83516770c97ed4a;hb=49d2b7459c5027557564b21e9487dadafbbbdc96;hp=e2b93316a4ade033f6ce4db3988cfd09cbf432e9;hpb=ee8403d4eb5760187d62b42a9cf4272de8fc0ec4;p=mothur.git

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index e2b9331..59dd0a5 100644
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -98,6 +98,28 @@ string ChimeraSlayerCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string ChimeraSlayerCommand::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 == "chimera") {  outputFileName =  "slayer.chimeras"; }
+            else if (type == "accnos") {  outputFileName =  "slayer.accnos"; }
+            else if (type == "fasta") {  outputFileName =  "slayer.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, "ChimeraSlayerCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 ChimeraSlayerCommand::ChimeraSlayerCommand(){	
 	try {
 		abort = true; calledHelp = true;
@@ -556,9 +578,9 @@ int ChimeraSlayerCommand::execute(){
 		
 			int start = time(NULL);	
 			if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]);  }//if user entered a file with a path then preserve it				
-			string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.chimera";
-			string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "slayer.accnos";
-			string trimFastaFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "slayer.fasta";		
+			string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("chimera");
+			string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("accnos");
+			string trimFastaFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("fasta");		
 			
 			//clears files
 			ofstream out, out1, out2;