Revert to previous commit

[mothur.git] / treereader.cpp

diff --git a/treereader.cpp b/treereader.cpp
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+++ b/treereader.cpp
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+//
+//  treereader.cpp
+//  Mothur
+//
+//  Created by Sarah Westcott on 4/11/12.
+//  Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+#include "treereader.h"
+#include "readtree.h"
+
+/***********************************************************************/
+
+TreeReader::TreeReader(string tf) : treefile(tf)  { 
+    try {
+        m = MothurOut::getInstance();
+        namefile = "";
+        groupfile = "";
+        readTrees();
+    }
+       catch(exception& e) {
+               m->errorOut(e, "TreeReader", "TreeReader");
+               exit(1);
+       }
+}
+/***********************************************************************/
+
+TreeReader::TreeReader(string tf, string gf) : treefile(tf),  groupfile(gf)  { 
+    try {
+        m = MothurOut::getInstance();
+        namefile = "";
+        readTrees();
+    }
+       catch(exception& e) {
+               m->errorOut(e, "TreeReader", "TreeReader");
+               exit(1);
+       }
+}
+/***********************************************************************/
+TreeReader::TreeReader(string tf, string gf, string nf) : treefile(tf),  groupfile(gf), namefile(nf)  { 
+    try {
+        m = MothurOut::getInstance();
+        readTrees();
+    }
+       catch(exception& e) {
+               m->errorOut(e, "TreeReader", "TreeReader");
+               exit(1);
+       }
+}
+/***********************************************************************/
+bool TreeReader::readTrees()  { 
+    try {
+        
+        tmap = new TreeMap();
+        if (groupfile != "") {      tmap->readMap(groupfile);        }
+               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
+                       for (int i = 0; i < m->Treenames.size(); i++) { tmap->addSeq(m->Treenames[i], "Group1"); }
+               }
+               
+        int numUniquesInName = 0;
+               if (namefile != "") { numUniquesInName = readNamesFile(); }
+               
+               ReadTree* read = new ReadNewickTree(treefile);
+               int readOk = read->read(tmap); 
+               
+               if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine();  delete read; m->control_pressed=true; return 0; }
+               
+               read->AssembleTrees(names);
+               trees = 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 (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) { for (int i = 0; i < trees.size(); i++) { delete trees[i]; } 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
+                                       }
+                               }
+                       }
+               }
+        
+        return true;
+    }
+       catch(exception& e) {
+               m->errorOut(e, "TreeReader", "readTrees");
+               exit(1);
+       }
+}
+/*****************************************************************/
+int TreeReader::readNamesFile() {
+       try {
+               nameMap.clear();
+        names.clear();
+               int 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 = nameMap.find(first);
+                       if (itNames == nameMap.end()) {  
+                               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]] = first; 
+                                       if ((groupfile == "") && (i != 0)) { tmap->addSeq(dupNames[i], "Group1"); } 
+                               }
+                       }else {  m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); nameMap.clear(); names.clear(); namefile = ""; return 1; }                    
+               }
+               in.close();
+               
+               return numUniquesInName;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "TreeReader", "readNamesFile");
+               exit(1);
+       }
+}
+/***********************************************************************/
+
+