X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=parsimonycommand.cpp;h=f124b6002ee2c247db14716b4be81cb9ec10d8f2;hp=50e1bfa7e590d6e2fa47b4c184700b440cdb9621;hb=49d2b7459c5027557564b21e9487dadafbbbdc96;hpb=ee8403d4eb5760187d62b42a9cf4272de8fc0ec4

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index 50e1bfa..f124b60 100644
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -52,6 +52,27 @@ string ParsimonyCommand::getHelpString(){
 		exit(1);
 	}
 }
+//**********************************************************************************************************************
+string ParsimonyCommand::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 == "parsimony") {  outputFileName =  "parsimony"; }
+            else if (type == "psummary") {  outputFileName =  "psummary"; }
+            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, "ParsimonyCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
 
 //**********************************************************************************************************************
 ParsimonyCommand::ParsimonyCommand(){	
@@ -204,11 +225,11 @@ int ParsimonyCommand::execute() {
             delete reader;
 	
 			if(outputDir == "") { outputDir += m->hasPath(treefile); }
-			output = new ColumnFile(outputDir + m->getSimpleName(treefile)  +  ".parsimony", itersString);
-			outputNames.push_back(outputDir + m->getSimpleName(treefile)  +  ".parsimony");
-			outputTypes["parsimony"].push_back(outputDir + m->getSimpleName(treefile)  +  ".parsimony");
+			output = new ColumnFile(outputDir + m->getSimpleName(treefile)  +  "." + getOutputFileNameTag("parsimony"), itersString);
+			outputNames.push_back(outputDir + m->getSimpleName(treefile)  +  "." + getOutputFileNameTag("parsimony"));
+			outputTypes["parsimony"].push_back(outputDir + m->getSimpleName(treefile)  + "." + getOutputFileNameTag("parsimony"));
 				
-			sumFile = outputDir + m->getSimpleName(treefile) + ".psummary";
+			sumFile = outputDir + m->getSimpleName(treefile) + "." + getOutputFileNameTag("psummary");
 			m->openOutputFile(sumFile, outSum);
 			outputNames.push_back(sumFile);
 			outputTypes["psummary"].push_back(sumFile);