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         groupFileName = filename;
  16         openInputFile(filename, fileHandle);
  17         index = 0;
  18 }
  19
  20 /************************************************************/
  21  GroupMap::~GroupMap(){}
  22
  23 /************************************************************/
  24 int GroupMap::readMap() {
  25                 string seqName, seqGroup;
  26                 int error = 0;
  27
  28                 while(fileHandle){
  29                         fileHandle >> seqName;                  //read from first column
  30                         fileHandle >> seqGroup;                 //read from second column
  31
  32                         setNamesOfGroups(seqGroup);
  33
  34                         it = groupmap.find(seqName);
  35
  36                         if (it != groupmap.end()) { error = 1; mothurOut("Your groupfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); mothurOutEndLine();  }
  37                         else {
  38                                 groupmap[seqName] = seqGroup;   //store data in map
  39                                 seqsPerGroup[seqGroup]++;  //increment number of seqs in that group
  40                         }
  41                         gobble(fileHandle);
  42                 }
  43                 fileHandle.close();
  44                 return error;
  45 }
  46 /************************************************************/
  47 int GroupMap::getNumGroups() { return namesOfGroups.size();     }
  48 /************************************************************/
  49
  50 string GroupMap::getGroup(string sequenceName) {
  51
  52         it = groupmap.find(sequenceName);
  53         if (it != groupmap.end()) { //sequence name was in group file
  54                 return it->second;
  55         }else {
  56                 return "not found";
  57         }
  58 }
  59
  60 /************************************************************/
  61 void GroupMap::setGroup(string sequenceName, string groupN) {
  62         groupmap[sequenceName] = groupN;
  63 }
  64 /************************************************************/
  65 void GroupMap::setNamesOfGroups(string seqGroup) {
  66                         int i, count;
  67                         count = 0;
  68                         for (i=0; i<namesOfGroups.size(); i++) {
  69                                 if (namesOfGroups[i] != seqGroup) {
  70                                         count++; //you have not found this group
  71                                 }else {
  72                                         break; //you already have it
  73                                 }
  74                         }
  75                         if (count == namesOfGroups.size()) {
  76                                 namesOfGroups.push_back(seqGroup); //new group
  77                                 seqsPerGroup[seqGroup] = 0;
  78                                 groupIndex[seqGroup] = index;
  79                                 index++;
  80                         }
  81 }
  82 /************************************************************/
  83 bool GroupMap::isValidGroup(string groupname) {
  84         try {
  85                 for (int i = 0; i < namesOfGroups.size(); i++) {
  86                         if (groupname == namesOfGroups[i]) { return true; }
  87                 }
  88
  89                 return false;
  90         }
  91         catch(exception& e) {
  92                 errorOut(e, "GroupMap", "isValidGroup");
  93                 exit(1);
  94         }
  95 }
  96 /************************************************************/
  97 int GroupMap::getNumSeqs(string group) {
  98         try {
  99
 100                 map<string, int>::iterator itNum;
 101
 102                 itNum = seqsPerGroup.find(group);
 103
 104                 if (itNum == seqsPerGroup.end()) { return 0; }
 105
 106                 return seqsPerGroup[group];
 107
 108         }
 109         catch(exception& e) {
 110                 errorOut(e, "GroupMap", "getNumSeqs");
 111                 exit(1);
 112         }
 113 }
 114
 115 /************************************************************/
 116 vector<string> GroupMap::getNamesSeqs(){
 117         try {
 118
 119                 vector<string> names;
 120
 121                 for (it = groupmap.begin(); it != groupmap.end(); it++) {
 122                         names.push_back(it->first);
 123                 }
 124
 125                 return names;
 126         }
 127         catch(exception& e) {
 128                 errorOut(e, "GroupMap", "getNamesSeqs");
 129                 exit(1);
 130         }
 131 }
 132 /************************************************************/
 133