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

[mothur.git] / classifytreecommand.cpp

diff --git a/classifytreecommand.cpp b/classifytreecommand.cpp
index 9ec4e6f89a40d12a1661144f8835cd6e1a4ccc84..bcf27698ce2bf68bf3dc6a3909228a9d4ccd5cb2 100644 (file)
--- a/classifytreecommand.cpp
+++ b/classifytreecommand.cpp
@@ -8,6 +8,7 @@
 
 #include "classifytreecommand.h"
 #include "phylotree.h"
+#include "treereader.h"
 
 //**********************************************************************************************************************
 vector<string> ClassifyTreeCommand::setParameters(){   
@@ -86,12 +87,6 @@ ClassifyTreeCommand::ClassifyTreeCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
-                       m->runParse = true;
-                       m->clearGroups();
-                       m->clearAllGroups();
-                       m->Treenames.clear();
-                       m->names.clear();
-                       
                        vector<string> tempOutNames;
                        outputTypes["tree"] = tempOutNames;
                        outputTypes["summary"] = tempOutNames;
@@ -195,74 +190,19 @@ int ClassifyTreeCommand::execute(){
                //    reading tree info                                                    //
                /***************************************************/
         m->setTreeFile(treefile);
-        if (groupfile != "") {
-                       //read in group map info.
-                       tmap = new TreeMap(groupfile);
-                       tmap->readMap();
-               }else{ //fake out by putting everyone in one group
-                       Tree* tree = new Tree(treefile); delete tree;  //extracts names from tree to make faked out groupmap
-                       tmap = new TreeMap();
-                       
-                       for (int i = 0; i < m->Treenames.size(); i++) { tmap->addSeq(m->Treenames[i], "Group1"); }
-               }
-               
-               if (namefile != "") { readNamesFile(); }
-               
-               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();
-        Tree* outputTree = T[0]; 
-               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 (namefile != "")  {  
-                       if (numUniquesInName == m->Treenames.size()) {  numNamesInTree = nameMap.size();  }
-                       else {   numNamesInTree = m->Treenames.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, groupfile, namefile);
+        vector<Tree*> T = reader->getTrees();
+        TreeMap* tmap = T[0]->getTreeMap();
+        Tree* outputTree = T[0];
+        delete reader;
+
+        if (namefile != "") { readNamesFile(); }
                         
-        if (m->control_pressed) { delete outputTree; delete tmap;  return 0; }
+        if (m->control_pressed) { delete tmap;  delete outputTree;  return 0; }
                
         readTaxonomyFile();
         
-        
         /***************************************************/
         //             get concensus taxonomies                    //
         /***************************************************/
@@ -484,6 +424,7 @@ map<string, set<string> > ClassifyTreeCommand::getDescendantList(Tree*& T, int i
                
                int lc = T->tree[i].getLChild();
                int rc = T->tree[i].getRChild();
+        TreeMap* tmap = T->getTreeMap();
                
                if (lc == -1) { //you are a leaf your only descendant is yourself
             string group = tmap->getGroup(T->tree[i].getName());