treemap.cpp

   1 /*
   2  *  treemap.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 1/26/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "treemap.h"
  11
  12 /************************************************************/
  13
  14  TreeMap::TreeMap(string filename) {
  15         groupFileName = filename;
  16         openInputFile(filename, fileHandle);
  17 }
  18
  19 /************************************************************/
  20  TreeMap::~TreeMap(){};
  21
  22 /************************************************************/
  23 void TreeMap::readMap() {
  24                 string seqName, seqGroup;
  25
  26                 while(fileHandle){
  27                         fileHandle >> seqName;                  //read from first column
  28                         fileHandle >> seqGroup;                 //read from second column
  29
  30                         namesOfSeqs.push_back(seqName);
  31                         setNamesOfGroups(seqGroup);
  32
  33                         treemap[seqName].groupname = seqGroup;  //store data in map
  34
  35                         it2 = seqsPerGroup.find(seqGroup);
  36                         if (it2 == seqsPerGroup.end()) { //if it's a new group
  37                                 seqsPerGroup[seqGroup] = 1;
  38                         }else {//it's a group we already have
  39                                 seqsPerGroup[seqGroup]++;
  40                         }
  41
  42                         gobble(fileHandle);
  43                 }
  44                 fileHandle.close();
  45 }
  46 /************************************************************/
  47
  48 int TreeMap::getNumGroups() {
  49
  50         return seqsPerGroup.size();
  51
  52 }
  53 /************************************************************/
  54
  55 int TreeMap::getNumSeqs() {
  56
  57         return namesOfSeqs.size();
  58
  59 }
  60
  61 /************************************************************/
  62
  63 string TreeMap::getGroup(string sequenceName) {
  64
  65         it = treemap.find(sequenceName);
  66         if (it != treemap.end()) { //sequence name was in group file
  67                 return it->second.groupname;
  68         }else {
  69                 return "not found";
  70         }
  71
  72 }
  73 /************************************************************/
  74 void TreeMap::setIndex(string seq, int index) {
  75         treemap[seq].vectorIndex = index;
  76 }
  77 /************************************************************/
  78 int TreeMap::getIndex(string seq) {
  79
  80         it = treemap.find(seq);
  81         // if it is a valid sequence name then return index
  82         if (it != treemap.end()) { return treemap[seq].vectorIndex; }
  83         // if not return error code
  84         else { return -1; }
  85
  86 }
  87 /************************************************************/
  88
  89 void TreeMap::setNamesOfGroups(string seqGroup) {
  90                         int i, count;
  91                         count = 0;
  92                         for (i=0; i<namesOfGroups.size(); i++) {
  93                                 if (namesOfGroups[i] != seqGroup) {
  94                                         count++; //you have not found this group
  95                                 }else {
  96                                         break; //you already have it
  97                                 }
  98                         }
  99                         if (count == namesOfGroups.size()) {
 100                                 namesOfGroups.push_back(seqGroup); //new group
 101                         }
 102 }
 103
 104 /***********************************************************************/
 105
 106 void TreeMap::print(ostream& output){
 107         try {
 108
 109                 for(it = treemap.begin(); it != treemap.end(); it++){
 110                         output << it->first << '\t' << it->second.groupname << '\t' << it->second.vectorIndex << endl;
 111                 }
 112         }
 113         catch(exception& e) {
 114                 cout << "Standard Error: " << e.what() << " has occurred in the TreeMap class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 115                 exit(1);
 116         }
 117         catch(...) {
 118                 cout << "An unknown error has occurred in the TreeMap class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 119                 exit(1);
 120         }
 121 }
 122
 123 /************************************************************/