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 void GroupMap::readMap() {
  25                 string seqName, seqGroup;
  26
  27                 while(fileHandle){
  28                         fileHandle >> seqName;                  //read from first column
  29                         fileHandle >> seqGroup;                 //read from second column
  30
  31                         setNamesOfGroups(seqGroup);
  32
  33                         groupmap[seqName] = seqGroup;   //store data in map
  34
  35                         gobble(fileHandle);
  36                 }
  37                 fileHandle.close();
  38 }
  39 /************************************************************/
  40 int GroupMap::getNumGroups() { return namesOfGroups.size();     }
  41 /************************************************************/
  42
  43 string GroupMap::getGroup(string sequenceName) {
  44
  45         it = groupmap.find(sequenceName);
  46         if (it != groupmap.end()) { //sequence name was in group file
  47                 return it->second;
  48         }else {
  49                 return "not found";
  50         }
  51 }
  52
  53 /************************************************************/
  54 void GroupMap::setGroup(string sequenceName, string groupN) {
  55         groupmap[sequenceName] = groupN;
  56 }
  57 /************************************************************/
  58 void GroupMap::setNamesOfGroups(string seqGroup) {
  59                         int i, count;
  60                         count = 0;
  61                         for (i=0; i<namesOfGroups.size(); i++) {
  62                                 if (namesOfGroups[i] != seqGroup) {
  63                                         count++; //you have not found this group
  64                                 }else {
  65                                         break; //you already have it
  66                                 }
  67                         }
  68                         if (count == namesOfGroups.size()) {
  69                                 namesOfGroups.push_back(seqGroup); //new group
  70                                 groupIndex[seqGroup] = index;
  71                                 index++;
  72                         }
  73 }
  74 /************************************************************/
  75 bool GroupMap::isValidGroup(string groupname) {
  76         try {
  77                 for (int i = 0; i < namesOfGroups.size(); i++) {
  78                         if (groupname == namesOfGroups[i]) { return true; }
  79                 }
  80
  81                 return false;
  82         }
  83         catch(exception& e) {
  84                 cout << "Standard Error: " << e.what() << " has occurred in the GroupMap class Function isValidGroup. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  85                 exit(1);
  86         }
  87         catch(...) {
  88                 cout << "An unknown error has occurred in the GroupMap class function isValidGroup. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  89                 exit(1);
  90         }
  91 }