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         index = 0;
  18 }
  19
  20 /************************************************************/
  21  GroupMap::~GroupMap(){};
  22
  23 /************************************************************/
  24 void GroupMap::readMap() {
  25                 string seqName, seqGroup;
  26
  27                 while(fileHandle){
  28                         fileHandle >> seqName;                  //read from first column
  29                         fileHandle >> seqGroup;                 //read from second column
  30
  31                         setNamesOfGroups(seqGroup);
  32
  33                         groupmap[seqName] = seqGroup;   //store data in map
  34
  35                         gobble(fileHandle);
  36                 }
  37                 fileHandle.close();
  38 }
  39 /************************************************************/
  40
  41 int GroupMap::getNumGroups() {
  42
  43         return namesOfGroups.size();
  44
  45 }
  46 /************************************************************/
  47
  48 string GroupMap::getGroup(string sequenceName) {
  49
  50         it = groupmap.find(sequenceName);
  51         if (it != groupmap.end()) { //sequence name was in group file
  52                 return it->second;
  53         }else {
  54                 return "not found";
  55         }
  56
  57 }
  58
  59 /************************************************************/
  60
  61 void GroupMap::setNamesOfGroups(string seqGroup) {
  62                         int i, count;
  63                         count = 0;
  64                         for (i=0; i<namesOfGroups.size(); i++) {
  65                                 if (namesOfGroups[i] != seqGroup) {
  66                                         count++; //you have not found this group
  67                                 }else {
  68                                         break; //you already have it
  69                                 }
  70                         }
  71                         if (count == namesOfGroups.size()) {
  72                                 namesOfGroups.push_back(seqGroup); //new group
  73                                 groupIndex[seqGroup] = index;
  74                                 index++;
  75                         }
  76 }