source/treereader.cpp

   1 //
   2 //  treereader.cpp
   3 //  Mothur
   4 //
   5 //  Created by Sarah Westcott on 4/11/12.
   6 //  Copyright (c) 2012 Schloss Lab. All rights reserved.
   7 //
   8
   9 #include "treereader.h"
  10 #include "readtree.h"
  11
  12 /***********************************************************************/
  13
  14 TreeReader::TreeReader(string tf) : treefile(tf)  {
  15     try {
  16         m = MothurOut::getInstance();
  17         namefile = "";
  18         groupfile = "";
  19         readTrees();
  20     }
  21         catch(exception& e) {
  22                 m->errorOut(e, "TreeReader", "TreeReader");
  23                 exit(1);
  24         }
  25 }
  26 /***********************************************************************/
  27
  28 TreeReader::TreeReader(string tf, string gf) : treefile(tf),  groupfile(gf)  {
  29     try {
  30         m = MothurOut::getInstance();
  31         namefile = "";
  32         readTrees();
  33     }
  34         catch(exception& e) {
  35                 m->errorOut(e, "TreeReader", "TreeReader");
  36                 exit(1);
  37         }
  38 }
  39 /***********************************************************************/
  40 TreeReader::TreeReader(string tf, string gf, string nf) : treefile(tf),  groupfile(gf), namefile(nf)  {
  41     try {
  42         m = MothurOut::getInstance();
  43         readTrees();
  44     }
  45         catch(exception& e) {
  46                 m->errorOut(e, "TreeReader", "TreeReader");
  47                 exit(1);
  48         }
  49 }
  50 /***********************************************************************/
  51 bool TreeReader::readTrees()  {
  52     try {
  53
  54         tmap = new TreeMap();
  55         if (groupfile != "") {      tmap->readMap(groupfile);        }
  56                 else{ //fake out by putting everyone in one group
  57                         Tree* tree = new Tree(treefile); delete tree;  //extracts names from tree to make faked out groupmap
  58                         for (int i = 0; i < m->Treenames.size(); i++) { tmap->addSeq(m->Treenames[i], "Group1"); }
  59                 }
  60
  61         int numUniquesInName = 0;
  62                 if (namefile != "") { numUniquesInName = readNamesFile(); }
  63
  64                 ReadTree* read = new ReadNewickTree(treefile);
  65                 int readOk = read->read(tmap);
  66
  67                 if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine();  delete read; m->control_pressed=true; return 0; }
  68
  69                 read->AssembleTrees(names);
  70                 trees = read->getTrees();
  71                 delete read;
  72
  73                 //make sure all files match
  74                 //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.
  75                 int numNamesInTree;
  76                 if (namefile != "")  {
  77                         if (numUniquesInName == m->Treenames.size()) {  numNamesInTree = nameMap.size();  }
  78                         else {   numNamesInTree = m->Treenames.size();  }
  79                 }else {  numNamesInTree = m->Treenames.size();  }
  80
  81
  82                 //output any names that are in group file but not in tree
  83                 if (numNamesInTree < tmap->getNumSeqs()) {
  84                         for (int i = 0; i < tmap->namesOfSeqs.size(); i++) {
  85                                 //is that name in the tree?
  86                                 int count = 0;
  87                                 for (int j = 0; j < m->Treenames.size(); j++) {
  88                                         if (tmap->namesOfSeqs[i] == m->Treenames[j]) { break; } //found it
  89                                         count++;
  90                                 }
  91
  92                                 if (m->control_pressed) { for (int i = 0; i < trees.size(); i++) { delete trees[i]; } return 0; }
  93
  94                                 //then you did not find it so report it
  95                                 if (count == m->Treenames.size()) {
  96                                         //if it is in your namefile then don't remove
  97                                         map<string, string>::iterator it = nameMap.find(tmap->namesOfSeqs[i]);
  98
  99                                         if (it == nameMap.end()) {
 100                                                 m->mothurOut(tmap->namesOfSeqs[i] + " is in your groupfile and not in your tree. It will be disregarded."); m->mothurOutEndLine();
 101                                                 tmap->removeSeq(tmap->namesOfSeqs[i]);
 102                                                 i--; //need this because removeSeq removes name from namesOfSeqs
 103                                         }
 104                                 }
 105                         }
 106                 }
 107
 108         return true;
 109     }
 110         catch(exception& e) {
 111                 m->errorOut(e, "TreeReader", "readTrees");
 112                 exit(1);
 113         }
 114 }
 115 /*****************************************************************/
 116 int TreeReader::readNamesFile() {
 117         try {
 118                 nameMap.clear();
 119         names.clear();
 120                 int numUniquesInName = 0;
 121
 122                 ifstream in;
 123                 m->openInputFile(namefile, in);
 124
 125                 string first, second;
 126                 map<string, string>::iterator itNames;
 127
 128                 while(!in.eof()) {
 129                         in >> first >> second; m->gobble(in);
 130
 131                         numUniquesInName++;
 132
 133                         itNames = nameMap.find(first);
 134                         if (itNames == nameMap.end()) {
 135                                 names[first] = second;
 136
 137                                 //we need a list of names in your namefile to use above when removing extra seqs above so we don't remove them
 138                                 vector<string> dupNames;
 139                                 m->splitAtComma(second, dupNames);
 140
 141                                 for (int i = 0; i < dupNames.size(); i++) {
 142                                         nameMap[dupNames[i]] = first;
 143                                         if ((groupfile == "") && (i != 0)) { tmap->addSeq(dupNames[i], "Group1"); }
 144                                 }
 145                         }else {  m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); nameMap.clear(); names.clear(); namefile = ""; return 1; }
 146                 }
 147                 in.close();
 148
 149                 return numUniquesInName;
 150         }
 151         catch(exception& e) {
 152                 m->errorOut(e, "TreeReader", "readNamesFile");
 153                 exit(1);
 154         }
 155 }
 156 /***********************************************************************/
 157
 158