X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=deuniquetreecommand.cpp;h=d334f8f4ef107d12a57eaa4aff4d71b84808edb9;hb=96dbe925073caefaed6e6db85659c144a806aeb1;hp=dca81e5ebb6359752731b7a003173b2da0306b0e;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607;p=mothur.git

diff --git a/deuniquetreecommand.cpp b/deuniquetreecommand.cpp
index dca81e5..d334f8f 100644
--- a/deuniquetreecommand.cpp
+++ b/deuniquetreecommand.cpp
@@ -8,6 +8,7 @@
  */
 
 #include "deuniquetreecommand.h"
+#include "treereader.h"
 
 //**********************************************************************************************************************
 vector<string> DeuniqueTreeCommand::setParameters(){	
@@ -42,6 +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; 
@@ -103,13 +124,7 @@ DeuniqueTreeCommand::DeuniqueTreeCommand(string option)  {
 				}
 			}
 			
-			m->runParse = true;
-			m->Groups.clear();
-			m->namesOfGroups.clear();
-			m->Treenames.clear();
-			m->names.clear();
-			
-			//check for required parameters
+            //check for required parameters
 			treefile = validParameter.validFile(parameters, "tree", true);
 			if (treefile == "not open") { abort = true; }
 			else if (treefile == "not found") { 				//if there is a current design file, use it
@@ -144,72 +159,22 @@ int DeuniqueTreeCommand::execute() {
 		
 		m->setTreeFile(treefile);
 		
-		//extracts names from tree to make faked out groupmap
-		Tree* tree = new Tree(treefile); delete tree;  
-		tmap = new TreeMap();
-		for (int i = 0; i < m->Treenames.size(); i++) { tmap->addSeq(m->Treenames[i], "Group1"); }
-		
-		if (m->control_pressed) {  delete tmap;  return 0; }
-		
-		readNamesFile(); 
-		
-		if (m->control_pressed) {  delete tmap;  return 0; }
-		
-		ReadTree* read = new ReadNewickTree(treefile);
-		int readOk = read->read(tmap); 
-		if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); delete tmap; delete read; return 0; }
-		
-		read->AssembleTrees();
-		vector<Tree*> T = read->getTrees();
-		delete read;
-		
-		//make sure all files match
-		//if you provide a namefile we will use the numNames in the namefile as long as the number of unique match the tree names size.
-		int numNamesInTree;
-		if (numUniquesInName == m->Treenames.size()) {  numNamesInTree = nameMap.size();  }
-		else {   numNamesInTree = m->Treenames.size();  }
-		
-		//output any names that are in group file but not in tree
-		if (numNamesInTree < tmap->getNumSeqs()) {
-			for (int i = 0; i < tmap->namesOfSeqs.size(); i++) {
-				//is that name in the tree?
-				int count = 0;
-				for (int j = 0; j < m->Treenames.size(); j++) {
-					if (tmap->namesOfSeqs[i] == m->Treenames[j]) { break; } //found it
-					count++;
-				}
-				
-				if (m->control_pressed) { 
-					delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
-					for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
-					m->Groups.clear();
-					return 0;
-				}
-				
-				//then you did not find it so report it 
-				if (count == m->Treenames.size()) { 
-					//if it is in your namefile then don't remove
-					map<string, string>::iterator it = nameMap.find(tmap->namesOfSeqs[i]);
-					
-					if (it == nameMap.end()) {
-						m->mothurOut(tmap->namesOfSeqs[i] + " is in your groupfile and not in your tree. It will be disregarded."); m->mothurOutEndLine();
-						tmap->removeSeq(tmap->namesOfSeqs[i]);
-						i--; //need this because removeSeq removes name from namesOfSeqs
-					}
-				}
-			}
-		}
-		
+		TreeReader* reader = new TreeReader(treefile, "", namefile);
+        vector<Tree*> T = reader->getTrees();
+        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, "deunique");
+		T[0]->print(out, nameMap);
 		out.close();
 		
-		delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
+        delete (T[0]->getCountTable());
+		for (int i = 0; i < T.size(); i++) { delete T[i]; }
 				
 		//set phylip file as new current phylipfile
 		string current = "";
@@ -231,46 +196,6 @@ int DeuniqueTreeCommand::execute() {
 		exit(1);
 	}
 }
-/*****************************************************************/
-int DeuniqueTreeCommand::readNamesFile() {
-	try {
-		m->names.clear();
-		numUniquesInName = 0;
-		
-		ifstream in;
-		m->openInputFile(namefile, in);
-		
-		string first, second;
-		map<string, string>::iterator itNames;
-		
-		while(!in.eof()) {
-			in >> first >> second; m->gobble(in);
-			
-			numUniquesInName++;
-			
-			itNames = m->names.find(first);
-			if (itNames == m->names.end()) {  
-				m->names[first] = second; 
-				
-				//we need a list of names in your namefile to use above when removing extra seqs above so we don't remove them
-				vector<string> dupNames;
-				m->splitAtComma(second, dupNames);
-				
-				for (int i = 0; i < dupNames.size(); i++) {	
-					nameMap[dupNames[i]] = dupNames[i]; 
-					if (i != 0) { tmap->addSeq(dupNames[i], "Group1"); } 
-				}
-			}else {  m->mothurOut(first + " has already been seen in namefile, aborting."); m->mothurOutEndLine(); in.close(); m->names.clear(); m->control_pressed = true; return 1; }			
-		}
-		in.close();
-		
-		return 0;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "DeuniqueTreeCommand", "readNamesFile");
-		exit(1);
-	}
-}
 /***********************************************************/