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                         gobble(fileHandle);
  36                 }
  37                 fileHandle.close();
  38 }
  39 /************************************************************/
  40
  41 int TreeMap::getNumGroups() {
  42
  43         return namesOfGroups.size();
  44
  45 }
  46 /************************************************************/
  47
  48 int TreeMap::getNumSeqs() {
  49
  50         return namesOfSeqs.size();
  51
  52 }
  53
  54 /************************************************************/
  55
  56 string TreeMap::getGroup(string sequenceName) {
  57
  58         it = treemap.find(sequenceName);
  59         if (it != treemap.end()) { //sequence name was in group file
  60                 return it->second.groupname;
  61         }else {
  62                 return "not found";
  63         }
  64
  65 }
  66 /************************************************************/
  67 void TreeMap::setIndex(string seq, int index) {
  68         treemap[seq].vectorIndex = index;
  69 }
  70 /************************************************************/
  71 int TreeMap::getIndex(string seq) {
  72
  73         it = treemap.find(seq);
  74         // if it is a valid sequence name then return index
  75         if (it != treemap.end()) { return treemap[seq].vectorIndex; }
  76         // if not return error code
  77         else { return -1; }
  78
  79 }
  80 /************************************************************/
  81
  82 void TreeMap::setNamesOfGroups(string seqGroup) {
  83                         int i, count;
  84                         count = 0;
  85                         for (i=0; i<namesOfGroups.size(); i++) {
  86                                 if (namesOfGroups[i] != seqGroup) {
  87                                         count++; //you have not found this group
  88                                 }else {
  89                                         break; //you already have it
  90                                 }
  91                         }
  92                         if (count == namesOfGroups.size()) {
  93                                 namesOfGroups.push_back(seqGroup); //new group
  94                         }
  95 }
  96
  97 /***********************************************************************/
  98
  99 void TreeMap::print(ostream& output){
 100         try {
 101
 102                 for(it = treemap.begin(); it != treemap.end(); it++){
 103                         output << it->first << '\t' << it->second.groupname << '\t' << it->second.vectorIndex << endl;
 104                 }
 105         }
 106         catch(exception& e) {
 107                 cout << "Standard Error: " << e.what() << " has occurred in the TreeMap class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 108                 exit(1);
 109         }
 110         catch(...) {
 111                 cout << "An unknown error has occurred in the TreeMap class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 112                 exit(1);
 113         }
 114 }
 115
 116 /************************************************************/