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