added dups parameter to chimera.uchime. working on make.contigs command.

[mothur.git] / deuniquetreecommand.cpp

diff --git a/deuniquetreecommand.cpp b/deuniquetreecommand.cpp
index c33c8e4ce19014c0059a89469217993a3f2fe59d..d334f8f4ef107d12a57eaa4aff4d71b84808edb9 100644 (file)
--- 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