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         m = MothurOut::getInstance();
  16         groupFileName = filename;
  17         openInputFile(filename, fileHandle);
  18         index = 0;
  19 }
  20
  21 /************************************************************/
  22  GroupMap::~GroupMap(){}
  23
  24 /************************************************************/
  25 int GroupMap::readMap() {
  26                 string seqName, seqGroup;
  27                 int error = 0;
  28
  29                 while(fileHandle){
  30                         fileHandle >> seqName;                  //read from first column
  31                         fileHandle >> seqGroup;                 //read from second column
  32
  33                         setNamesOfGroups(seqGroup);
  34
  35                         it = groupmap.find(seqName);
  36
  37                         if (it != groupmap.end()) { error = 1; m->mothurOut("Your groupfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }
  38                         else {
  39                                 groupmap[seqName] = seqGroup;   //store data in map
  40                                 seqsPerGroup[seqGroup]++;  //increment number of seqs in that group
  41                         }
  42                         gobble(fileHandle);
  43                 }
  44                 fileHandle.close();
  45                 return error;
  46 }
  47 /************************************************************/
  48 int GroupMap::getNumGroups() { return namesOfGroups.size();     }
  49 /************************************************************/
  50
  51 string GroupMap::getGroup(string sequenceName) {
  52
  53         it = groupmap.find(sequenceName);
  54         if (it != groupmap.end()) { //sequence name was in group file
  55                 return it->second;
  56         }else {
  57                 return "not found";
  58         }
  59 }
  60
  61 /************************************************************/
  62 void GroupMap::setGroup(string sequenceName, string groupN) {
  63         groupmap[sequenceName] = groupN;
  64 }
  65 /************************************************************/
  66 void GroupMap::setNamesOfGroups(string seqGroup) {
  67                         int i, count;
  68                         count = 0;
  69                         for (i=0; i<namesOfGroups.size(); i++) {
  70                                 if (namesOfGroups[i] != seqGroup) {
  71                                         count++; //you have not found this group
  72                                 }else {
  73                                         break; //you already have it
  74                                 }
  75                         }
  76                         if (count == namesOfGroups.size()) {
  77                                 namesOfGroups.push_back(seqGroup); //new group
  78                                 seqsPerGroup[seqGroup] = 0;
  79                                 groupIndex[seqGroup] = index;
  80                                 index++;
  81                         }
  82 }
  83 /************************************************************/
  84 bool GroupMap::isValidGroup(string groupname) {
  85         try {
  86                 for (int i = 0; i < namesOfGroups.size(); i++) {
  87                         if (groupname == namesOfGroups[i]) { return true; }
  88                 }
  89
  90                 return false;
  91         }
  92         catch(exception& e) {
  93                 m->errorOut(e, "GroupMap", "isValidGroup");
  94                 exit(1);
  95         }
  96 }
  97 /************************************************************/
  98 int GroupMap::getNumSeqs(string group) {
  99         try {
 100
 101                 map<string, int>::iterator itNum;
 102
 103                 itNum = seqsPerGroup.find(group);
 104
 105                 if (itNum == seqsPerGroup.end()) { return 0; }
 106
 107                 return seqsPerGroup[group];
 108
 109         }
 110         catch(exception& e) {
 111                 m->errorOut(e, "GroupMap", "getNumSeqs");
 112                 exit(1);
 113         }
 114 }
 115
 116 /************************************************************/
 117 vector<string> GroupMap::getNamesSeqs(){
 118         try {
 119
 120                 vector<string> names;
 121
 122                 for (it = groupmap.begin(); it != groupmap.end(); it++) {
 123                         names.push_back(it->first);
 124                 }
 125
 126                 return names;
 127         }
 128         catch(exception& e) {
 129                 m->errorOut(e, "GroupMap", "getNamesSeqs");
 130                 exit(1);
 131         }
 132 }
 133 /************************************************************/
 134