X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=deuniquetreecommand.cpp;h=d334f8f4ef107d12a57eaa4aff4d71b84808edb9;hb=6c2b1e530a5c0bb87040e58a3e410097acdfcc3d;hp=c33c8e4ce19014c0059a89469217993a3f2fe59d;hpb=d2390ede25cc211f95f99e377d5654bad7e6950e;p=mothur.git

diff --git a/deuniquetreecommand.cpp b/deuniquetreecommand.cpp
index c33c8e4..d334f8f 100644
--- a/deuniquetreecommand.cpp
+++ b/deuniquetreecommand.cpp
@@ -43,6 +43,26 @@ string DeuniqueTreeCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string DeuniqueTreeCommand::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 == "tree") {  outputFileName =  "deunique.tre"; }
+            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, "DeuniqueTreeCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 DeuniqueTreeCommand::DeuniqueTreeCommand(){	
 	try {
 		abort = true; calledHelp = true; 
@@ -141,18 +161,19 @@ int DeuniqueTreeCommand::execute() {
 		
 		TreeReader* reader = new TreeReader(treefile, "", namefile);
         vector<Tree*> T = reader->getTrees();
-        map<string, string> nameMap = reader->getNameMap();
+        map<string, string> nameMap;
+        m->readNames(namefile, nameMap);
         delete reader;		
 		
 		//print new Tree
-		string outputFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + "deunique.tre";
+		string outputFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + getOutputFileNameTag("tree");
 		outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
 		ofstream out;
 		m->openOutputFile(outputFile, out);
 		T[0]->print(out, nameMap);
 		out.close();
 		
-        delete (T[0]->getTreeMap());
+        delete (T[0]->getCountTable());
 		for (int i = 0; i < T.size(); i++) { delete T[i]; }
 				
 		//set phylip file as new current phylipfile