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 int GroupMap::readDesignMap(string filename) {
  78     groupFileName = filename;
  79         m->openInputFile(filename, fileHandle);
  80         index = 0;
  81     string seqName, seqGroup;
  82     int error = 0;
  83
  84     while(fileHandle){
  85         fileHandle >> seqName;  m->gobble(fileHandle);          //read from first column
  86         fileHandle >> seqGroup;                 //read from second column
  87
  88         if (m->control_pressed) {  fileHandle.close();  return 1; }
  89
  90         setNamesOfGroups(seqGroup);
  91
  92         it = groupmap.find(seqName);
  93
  94         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();  }
  95         else {
  96             groupmap[seqName] = seqGroup;       //store data in map
  97             seqsPerGroup[seqGroup]++;  //increment number of seqs in that group
  98         }
  99         m->gobble(fileHandle);
 100     }
 101     fileHandle.close();
 102     m->setAllGroups(namesOfGroups);
 103     return error;
 104 }
 105 /************************************************************/
 106 int GroupMap::getNumGroups() { return namesOfGroups.size();     }
 107 /************************************************************/
 108
 109 string GroupMap::getGroup(string sequenceName) {
 110
 111         it = groupmap.find(sequenceName);
 112         if (it != groupmap.end()) { //sequence name was in group file
 113                 return it->second;
 114         }else {
 115                 return "not found";
 116         }
 117 }
 118
 119 /************************************************************/
 120
 121 void GroupMap::setGroup(string sequenceName, string groupN) {
 122         setNamesOfGroups(groupN);
 123
 124         it = groupmap.find(sequenceName);
 125
 126         if (it != groupmap.end()) {  m->mothurOut("Your groupfile contains more than 1 sequence named " + sequenceName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }
 127         else {
 128                 groupmap[sequenceName] = groupN;        //store data in map
 129                 seqsPerGroup[groupN]++;  //increment number of seqs in that group
 130         }
 131 }
 132
 133 /************************************************************/
 134 void GroupMap::setNamesOfGroups(string seqGroup) {
 135         int i, count;
 136         count = 0;
 137         for (i=0; i<namesOfGroups.size(); i++) {
 138                 if (namesOfGroups[i] != seqGroup) {
 139                         count++; //you have not found this group
 140                 }else {
 141                         break; //you already have it
 142                 }
 143         }
 144         if (count == namesOfGroups.size()) {
 145                 namesOfGroups.push_back(seqGroup); //new group
 146                 seqsPerGroup[seqGroup] = 0;
 147                 groupIndex[seqGroup] = index;
 148                 index++;
 149         }
 150 }
 151 /************************************************************/
 152 bool GroupMap::isValidGroup(string groupname) {
 153         try {
 154                 for (int i = 0; i < namesOfGroups.size(); i++) {
 155                         if (groupname == namesOfGroups[i]) { return true; }
 156                 }
 157
 158                 return false;
 159         }
 160         catch(exception& e) {
 161                 m->errorOut(e, "GroupMap", "isValidGroup");
 162                 exit(1);
 163         }
 164 }
 165 /************************************************************/
 166 int GroupMap::getNumSeqs(string group) {
 167         try {
 168
 169                 map<string, int>::iterator itNum;
 170
 171                 itNum = seqsPerGroup.find(group);
 172
 173                 if (itNum == seqsPerGroup.end()) { return 0; }
 174
 175                 return seqsPerGroup[group];
 176
 177         }
 178         catch(exception& e) {
 179                 m->errorOut(e, "GroupMap", "getNumSeqs");
 180                 exit(1);
 181         }
 182 }
 183
 184 /************************************************************/
 185 vector<string> GroupMap::getNamesSeqs(){
 186         try {
 187
 188                 vector<string> names;
 189
 190                 for (it = groupmap.begin(); it != groupmap.end(); it++) {
 191                         names.push_back(it->first);
 192                 }
 193
 194                 return names;
 195         }
 196         catch(exception& e) {
 197                 m->errorOut(e, "GroupMap", "getNamesSeqs");
 198                 exit(1);
 199         }
 200 }
 201 /************************************************************/
 202 vector<string> GroupMap::getNamesSeqs(vector<string> picked){
 203         try {
 204
 205                 vector<string> names;
 206
 207                 for (it = groupmap.begin(); it != groupmap.end(); it++) {
 208                         //if you are belong to one the the groups in the picked vector add you
 209                         if (m->inUsersGroups(it->second, picked)) {
 210                                 names.push_back(it->first);
 211                         }
 212                 }
 213
 214                 return names;
 215         }
 216         catch(exception& e) {
 217                 m->errorOut(e, "GroupMap", "getNamesSeqs");
 218                 exit(1);
 219         }
 220 }
 221
 222 /************************************************************/
 223