X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqsummarycommand.cpp;h=c328a041267d01e21ed2e99780f18de486571685;hb=49d2b7459c5027557564b21e9487dadafbbbdc96;hp=68d3bf583f9c7de2db85ebfa27a2fecdd7738922;hpb=43ed0accfbc2852849e104ff7eccdd2c42acd4ec;p=mothur.git

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index 68d3bf5..c328a04 100644
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -45,6 +45,26 @@ string SeqSummaryCommand::getHelpString(){
 		exit(1);
 	}
 }
+//**********************************************************************************************************************
+string SeqSummaryCommand::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 == "summary")            {   outputFileName =  "summary";   }
+            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, "SeqSummaryCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
 
 //**********************************************************************************************************************
 SeqSummaryCommand::SeqSummaryCommand(){	
@@ -155,7 +175,7 @@ int SeqSummaryCommand::execute(){
 		//set current fasta to fastafile
 		m->setFastaFile(fastafile);
 		
-		string summaryFile = outputDir + m->getSimpleName(fastafile) + ".summary";
+		string summaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("summary");
 				
 		int numSeqs = 0;
 		
@@ -414,7 +434,7 @@ int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<in
 					//make sure this sequence is in the namefile, else error 
 					map<string, int>::iterator it = nameMap.find(current.getName());
 					
-					if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + current.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
+					if (it == nameMap.end()) { m->mothurOut("[ERROR]: '" + current.getName() + "' is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
 					else { num = it->second; }
 				}