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                 m->namesOfGroups = namesOfGroups;
  48                 return error;
  49 }
  50 /************************************************************/
  51 int GroupMap::readDesignMap() {
  52                 string seqName, seqGroup;
  53                 int error = 0;
  54
  55                 while(fileHandle){
  56                         fileHandle >> seqName;  m->gobble(fileHandle);          //read from first column
  57                         fileHandle >> seqGroup;                 //read from second column
  58
  59                         if (m->control_pressed) {  fileHandle.close();  return 1; }
  60
  61                         setNamesOfGroups(seqGroup);
  62
  63                         it = groupmap.find(seqName);
  64
  65                         if (it != groupmap.end()) { error = 1; m->mothurOut("Your designfile contains more than 1 group named " + seqName + ", group names must be unique. Please correct."); m->mothurOutEndLine();  }
  66                         else {
  67                                 groupmap[seqName] = seqGroup;   //store data in map
  68                                 seqsPerGroup[seqGroup]++;  //increment number of seqs in that group
  69                         }
  70                         m->gobble(fileHandle);
  71                 }
  72                 fileHandle.close();
  73                 m->namesOfGroups = namesOfGroups;
  74                 return error;
  75 }
  76
  77 /************************************************************/
  78 int GroupMap::getNumGroups() { return namesOfGroups.size();     }
  79 /************************************************************/
  80
  81 string GroupMap::getGroup(string sequenceName) {
  82
  83         it = groupmap.find(sequenceName);
  84         if (it != groupmap.end()) { //sequence name was in group file
  85                 return it->second;
  86         }else {
  87                 return "not found";
  88         }
  89 }
  90
  91 /************************************************************/
  92
  93 void GroupMap::setGroup(string sequenceName, string groupN) {
  94         groupmap[sequenceName] = groupN;
  95 }
  96
  97 /************************************************************/
  98 void GroupMap::setNamesOfGroups(string seqGroup) {
  99         int i, count;
 100         count = 0;
 101         for (i=0; i<namesOfGroups.size(); i++) {
 102                 if (namesOfGroups[i] != seqGroup) {
 103                         count++; //you have not found this group
 104                 }else {
 105                         break; //you already have it
 106                 }
 107         }
 108         if (count == namesOfGroups.size()) {
 109                 namesOfGroups.push_back(seqGroup); //new group
 110                 seqsPerGroup[seqGroup] = 0;
 111                 groupIndex[seqGroup] = index;
 112                 index++;
 113         }
 114 }
 115 /************************************************************/
 116 bool GroupMap::isValidGroup(string groupname) {
 117         try {
 118                 for (int i = 0; i < namesOfGroups.size(); i++) {
 119                         if (groupname == namesOfGroups[i]) { return true; }
 120                 }
 121
 122                 return false;
 123         }
 124         catch(exception& e) {
 125                 m->errorOut(e, "GroupMap", "isValidGroup");
 126                 exit(1);
 127         }
 128 }
 129 /************************************************************/
 130 int GroupMap::getNumSeqs(string group) {
 131         try {
 132
 133                 map<string, int>::iterator itNum;
 134
 135                 itNum = seqsPerGroup.find(group);
 136
 137                 if (itNum == seqsPerGroup.end()) { return 0; }
 138
 139                 return seqsPerGroup[group];
 140
 141         }
 142         catch(exception& e) {
 143                 m->errorOut(e, "GroupMap", "getNumSeqs");
 144                 exit(1);
 145         }
 146 }
 147
 148 /************************************************************/
 149 vector<string> GroupMap::getNamesSeqs(){
 150         try {
 151
 152                 vector<string> names;
 153
 154                 for (it = groupmap.begin(); it != groupmap.end(); it++) {
 155                         names.push_back(it->first);
 156                 }
 157
 158                 return names;
 159         }
 160         catch(exception& e) {
 161                 m->errorOut(e, "GroupMap", "getNamesSeqs");
 162                 exit(1);
 163         }
 164 }
 165 /************************************************************/
 166 vector<string> GroupMap::getNamesSeqs(vector<string> picked){
 167         try {
 168
 169                 vector<string> names;
 170
 171                 for (it = groupmap.begin(); it != groupmap.end(); it++) {
 172                         //if you are belong to one the the groups in the picked vector add you
 173                         if (m->inUsersGroups(it->second, picked)) {
 174                                 names.push_back(it->first);
 175                         }
 176                 }
 177
 178                 return names;
 179         }
 180         catch(exception& e) {
 181                 m->errorOut(e, "GroupMap", "getNamesSeqs");
 182                 exit(1);
 183         }
 184 }
 185
 186 /************************************************************/
 187