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->setAllGroups(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->setAllGroups(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         setNamesOfGroups(groupN);
  95
  96         it = groupmap.find(sequenceName);
  97
  98         if (it != groupmap.end()) {  m->mothurOut("Your groupfile contains more than 1 sequence named " + sequenceName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }
  99         else {
 100                 groupmap[sequenceName] = groupN;        //store data in map
 101                 seqsPerGroup[groupN]++;  //increment number of seqs in that group
 102         }
 103 }
 104
 105 /************************************************************/
 106 void GroupMap::setNamesOfGroups(string seqGroup) {
 107         int i, count;
 108         count = 0;
 109         for (i=0; i<namesOfGroups.size(); i++) {
 110                 if (namesOfGroups[i] != seqGroup) {
 111                         count++; //you have not found this group
 112                 }else {
 113                         break; //you already have it
 114                 }
 115         }
 116         if (count == namesOfGroups.size()) {
 117                 namesOfGroups.push_back(seqGroup); //new group
 118                 seqsPerGroup[seqGroup] = 0;
 119                 groupIndex[seqGroup] = index;
 120                 index++;
 121         }
 122 }
 123 /************************************************************/
 124 bool GroupMap::isValidGroup(string groupname) {
 125         try {
 126                 for (int i = 0; i < namesOfGroups.size(); i++) {
 127                         if (groupname == namesOfGroups[i]) { return true; }
 128                 }
 129
 130                 return false;
 131         }
 132         catch(exception& e) {
 133                 m->errorOut(e, "GroupMap", "isValidGroup");
 134                 exit(1);
 135         }
 136 }
 137 /************************************************************/
 138 int GroupMap::getNumSeqs(string group) {
 139         try {
 140
 141                 map<string, int>::iterator itNum;
 142
 143                 itNum = seqsPerGroup.find(group);
 144
 145                 if (itNum == seqsPerGroup.end()) { return 0; }
 146
 147                 return seqsPerGroup[group];
 148
 149         }
 150         catch(exception& e) {
 151                 m->errorOut(e, "GroupMap", "getNumSeqs");
 152                 exit(1);
 153         }
 154 }
 155
 156 /************************************************************/
 157 vector<string> GroupMap::getNamesSeqs(){
 158         try {
 159
 160                 vector<string> names;
 161
 162                 for (it = groupmap.begin(); it != groupmap.end(); it++) {
 163                         names.push_back(it->first);
 164                 }
 165
 166                 return names;
 167         }
 168         catch(exception& e) {
 169                 m->errorOut(e, "GroupMap", "getNamesSeqs");
 170                 exit(1);
 171         }
 172 }
 173 /************************************************************/
 174 vector<string> GroupMap::getNamesSeqs(vector<string> picked){
 175         try {
 176
 177                 vector<string> names;
 178
 179                 for (it = groupmap.begin(); it != groupmap.end(); it++) {
 180                         //if you are belong to one the the groups in the picked vector add you
 181                         if (m->inUsersGroups(it->second, picked)) {
 182                                 names.push_back(it->first);
 183                         }
 184                 }
 185
 186                 return names;
 187         }
 188         catch(exception& e) {
 189                 m->errorOut(e, "GroupMap", "getNamesSeqs");
 190                 exit(1);
 191         }
 192 }
 193
 194 /************************************************************/
 195