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         m->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;  m->gobble(fileHandle);          //read from first column
  31                         fileHandle >> seqGroup;                 //read from second column
  32
  33                         if (m->control_pressed) {  fileHandle.close();  return 1; }
  34
  35                         setNamesOfGroups(seqGroup);
  36
  37                         it = groupmap.find(seqName);
  38
  39                         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();  }
  40                         else {
  41                                 groupmap[seqName] = seqGroup;   //store data in map
  42                                 seqsPerGroup[seqGroup]++;  //increment number of seqs in that group
  43                         }
  44                         m->gobble(fileHandle);
  45                 }
  46                 fileHandle.close();
  47                 return error;
  48 }
  49 /************************************************************/
  50 int GroupMap::getNumGroups() { return namesOfGroups.size();     }
  51 /************************************************************/
  52
  53 string GroupMap::getGroup(string sequenceName) {
  54
  55         it = groupmap.find(sequenceName);
  56         if (it != groupmap.end()) { //sequence name was in group file
  57                 return it->second;
  58         }else {
  59                 return "not found";
  60         }
  61 }
  62
  63 /************************************************************/
  64 void GroupMap::setGroup(string sequenceName, string groupN) {
  65         groupmap[sequenceName] = groupN;
  66 }
  67 /************************************************************/
  68 void GroupMap::setNamesOfGroups(string seqGroup) {
  69                         int i, count;
  70                         count = 0;
  71                         for (i=0; i<namesOfGroups.size(); i++) {
  72                                 if (namesOfGroups[i] != seqGroup) {
  73                                         count++; //you have not found this group
  74                                 }else {
  75                                         break; //you already have it
  76                                 }
  77                         }
  78                         if (count == namesOfGroups.size()) {
  79                                 namesOfGroups.push_back(seqGroup); //new group
  80                                 seqsPerGroup[seqGroup] = 0;
  81                                 groupIndex[seqGroup] = index;
  82                                 index++;
  83                         }
  84 }
  85 /************************************************************/
  86 bool GroupMap::isValidGroup(string groupname) {
  87         try {
  88                 for (int i = 0; i < namesOfGroups.size(); i++) {
  89                         if (groupname == namesOfGroups[i]) { return true; }
  90                 }
  91
  92                 return false;
  93         }
  94         catch(exception& e) {
  95                 m->errorOut(e, "GroupMap", "isValidGroup");
  96                 exit(1);
  97         }
  98 }
  99 /************************************************************/
 100 int GroupMap::getNumSeqs(string group) {
 101         try {
 102
 103                 map<string, int>::iterator itNum;
 104
 105                 itNum = seqsPerGroup.find(group);
 106
 107                 if (itNum == seqsPerGroup.end()) { return 0; }
 108
 109                 return seqsPerGroup[group];
 110
 111         }
 112         catch(exception& e) {
 113                 m->errorOut(e, "GroupMap", "getNumSeqs");
 114                 exit(1);
 115         }
 116 }
 117
 118 /************************************************************/
 119 vector<string> GroupMap::getNamesSeqs(){
 120         try {
 121
 122                 vector<string> names;
 123
 124                 for (it = groupmap.begin(); it != groupmap.end(); it++) {
 125                         names.push_back(it->first);
 126                 }
 127
 128                 return names;
 129         }
 130         catch(exception& e) {
 131                 m->errorOut(e, "GroupMap", "getNamesSeqs");
 132                 exit(1);
 133         }
 134 }
 135 /************************************************************/
 136