working on pam

[mothur.git] / deuniquetreecommand.cpp

diff --git a/deuniquetreecommand.cpp b/deuniquetreecommand.cpp
index 662282b1d05d57e25ee2c259f178d00c5ecf96ca..703e75f21be03d4cba59d994f68932301d84a946 100644 (file)
--- a/deuniquetreecommand.cpp
+++ b/deuniquetreecommand.cpp
@@ -13,10 +13,10 @@
 //**********************************************************************************************************************
 vector<string> DeuniqueTreeCommand::setParameters(){   
        try {
-               CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptree);
-               CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none","tree",false,true,true); parameters.push_back(ptree);
+               CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pname);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -43,24 +43,19 @@ string DeuniqueTreeCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
-string DeuniqueTreeCommand::getOutputFileNameTag(string type, string inputName=""){    
-       try {
-        string outputFileName = "";
-               map<string, vector<string> >::iterator it;
+string DeuniqueTreeCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
         
-        //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);
-       }
+        if (type == "tree") {  pattern = "[filename],deunique.tre"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "DeuniqueTreeCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 DeuniqueTreeCommand::DeuniqueTreeCommand(){    
@@ -161,18 +156,21 @@ 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)) + getOutputFileNameTag("tree");
+        map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(treefile));
+               string outputFile = getOutputFileName("tree", variables);
                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