X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=secondarystructurecommand.cpp;h=ee50ab14e6183af4b2fe9979c97336ac1d9b75a5;hb=f509429e06e545bde69c97cacc0eb436775bd329;hp=24142e0cf4aa6174a8006f1e0a7a85c82f10ab24;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;p=mothur.git

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index 24142e0..ee50ab1 100644
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -45,6 +45,26 @@ string AlignCheckCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string AlignCheckCommand::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 == "aligncheck")            {   outputFileName =  "align.check";   }
+            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, "AlignCheckCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 AlignCheckCommand::AlignCheckCommand(){	
 	try {
 		abort = true; calledHelp = true; 
@@ -170,7 +190,7 @@ int AlignCheckCommand::execute(){
 		m->openInputFile(fastafile, in);
 		
 		ofstream out;
-		string outfile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "align.check";
+		string outfile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("aligncheck");
 		m->openOutputFile(outfile, out);