added tree reader class to handle reading trees. Reworked the tree map to tree class...

[mothur.git] / deuniquetreecommand.cpp

diff --git a/deuniquetreecommand.cpp b/deuniquetreecommand.cpp
index 64ea9b700d3e7193fb3502ae2bd5dd160cb26297..c33c8e4ce19014c0059a89469217993a3f2fe59d 100644 (file)
--- a/deuniquetreecommand.cpp
+++ b/deuniquetreecommand.cpp
@@ -8,6 +8,7 @@
  */
 
 #include "deuniquetreecommand.h"
+#include "treereader.h"
 
 //**********************************************************************************************************************
 vector<string> DeuniqueTreeCommand::setParameters(){   
@@ -103,13 +104,7 @@ DeuniqueTreeCommand::DeuniqueTreeCommand(string option)  {
                                }
                        }
                        
-                       m->runParse = true;
-                       m->clearGroups();
-                       m->clearAllGroups();
-                       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 +139,21 @@ 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->clearGroups();
-                                       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 = reader->getNameMap();
+        delete reader;         
                
                //print new Tree
                string outputFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + "deunique.tre";
                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]->getTreeMap());
+               for (int i = 0; i < T.size(); i++) { delete T[i]; }
                                
                //set phylip file as new current phylipfile
                string current = "";
@@ -231,46 +175,6 @@ 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);
-       }
-}
 /***********************************************************/