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                         seqsPerGroup[seqGroup]++;  //increment number of seqs in that group
  35
  36                         gobble(fileHandle);
  37                 }
  38                 fileHandle.close();
  39 }
  40 /************************************************************/
  41 int GroupMap::getNumGroups() { return namesOfGroups.size();     }
  42 /************************************************************/
  43
  44 string GroupMap::getGroup(string sequenceName) {
  45
  46         it = groupmap.find(sequenceName);
  47         if (it != groupmap.end()) { //sequence name was in group file
  48                 return it->second;
  49         }else {
  50                 return "not found";
  51         }
  52 }
  53
  54 /************************************************************/
  55 void GroupMap::setGroup(string sequenceName, string groupN) {
  56         groupmap[sequenceName] = groupN;
  57 }
  58 /************************************************************/
  59 void GroupMap::setNamesOfGroups(string seqGroup) {
  60                         int i, count;
  61                         count = 0;
  62                         for (i=0; i<namesOfGroups.size(); i++) {
  63                                 if (namesOfGroups[i] != seqGroup) {
  64                                         count++; //you have not found this group
  65                                 }else {
  66                                         break; //you already have it
  67                                 }
  68                         }
  69                         if (count == namesOfGroups.size()) {
  70                                 namesOfGroups.push_back(seqGroup); //new group
  71                                 seqsPerGroup[seqGroup] = 0;
  72                                 groupIndex[seqGroup] = index;
  73                                 index++;
  74                         }
  75 }
  76 /************************************************************/
  77 bool GroupMap::isValidGroup(string groupname) {
  78         try {
  79                 for (int i = 0; i < namesOfGroups.size(); i++) {
  80                         if (groupname == namesOfGroups[i]) { return true; }
  81                 }
  82
  83                 return false;
  84         }
  85         catch(exception& e) {
  86                 errorOut(e, "GroupMap", "isValidGroup");
  87                 exit(1);
  88         }
  89 }
  90 /************************************************************/
  91 int GroupMap::getNumSeqs(string group) {
  92         try {
  93
  94                 map<string, int>::iterator itNum;
  95
  96                 itNum = seqsPerGroup.find(group);
  97
  98                 if (itNum == seqsPerGroup.end()) { return 0; }
  99
 100                 return seqsPerGroup[group];
 101
 102         }
 103         catch(exception& e) {
 104                 errorOut(e, "GroupMap", "getNumSeqs");
 105                 exit(1);
 106         }
 107 }
 108
 109 /************************************************************/
 110 vector<string> GroupMap::getNamesSeqs(){
 111         try {
 112
 113                 vector<string> names;
 114
 115                 for (it = groupmap.begin(); it != groupmap.end(); it++) {
 116                         names.push_back(it->first);
 117                 }
 118
 119                 return names;
 120         }
 121         catch(exception& e) {
 122                 errorOut(e, "GroupMap", "getNamesSeqs");
 123                 exit(1);
 124         }
 125 }
 126 /************************************************************/
 127