groupmap.cpp

   1 /*
   2  *  groupmap.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 12/1/08.
   6  *  Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "groupmap.h"
  11
  12 /************************************************************/
  13
  14  GroupMap::GroupMap(string filename) {
  15         groupFileName = filename;
  16         openInputFile(filename, fileHandle);
  17 }
  18
  19 /************************************************************/
  20  GroupMap::~GroupMap(){};
  21
  22 /************************************************************/
  23 void GroupMap::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                         setNamesOfGroups(seqGroup);
  31
  32                         groupmap[seqName] = seqGroup;   //store data in map
  33
  34                         gobble(fileHandle);
  35                 }
  36                 fileHandle.close();
  37 }
  38 /************************************************************/
  39
  40 int GroupMap::getNumGroups() {
  41
  42         return namesOfGroups.size();
  43
  44 }
  45 /************************************************************/
  46
  47 string GroupMap::getGroup(string sequenceName) {
  48
  49         it = groupmap.find(sequenceName);
  50         if (it != groupmap.end()) { //sequence name was in group file
  51                 return it->second;
  52         }else {
  53                 return "not found";
  54         }
  55
  56 }
  57
  58 /************************************************************/
  59
  60 void GroupMap::setNamesOfGroups(string seqGroup) {
  61                         int i, count;
  62                         count = 0;
  63                         for (i=0; i<namesOfGroups.size(); i++) {
  64                                 if (namesOfGroups[i] != seqGroup) {
  65                                         count++; //you have not found this group
  66                                 }else {
  67                                         break; //you already have it
  68                                 }
  69                         }
  70                         if (count == namesOfGroups.size()) {
  71                                 namesOfGroups.push_back(seqGroup); //new group
  72                         }
  73 }