treemap.cpp

   1 /*
   2  *  treemap.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 1/26/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "treemap.h"
  11
  12 /************************************************************/
  13
  14  TreeMap::TreeMap(string filename) {
  15         groupFileName = filename;
  16         openInputFile(filename, fileHandle);
  17 }
  18
  19 /************************************************************/
  20  TreeMap::~TreeMap(){}
  21
  22 /************************************************************/
  23 void TreeMap::readMap() {
  24                 string seqName, seqGroup;
  25
  26                 while(fileHandle){
  27                         fileHandle >> seqName;                  //read from first column
  28                         fileHandle >> seqGroup;                 //read from second column
  29
  30                         namesOfSeqs.push_back(seqName);
  31                         setNamesOfGroups(seqGroup);
  32
  33                         treemap[seqName].groupname = seqGroup;  //store data in map
  34
  35                         it2 = seqsPerGroup.find(seqGroup);
  36                         if (it2 == seqsPerGroup.end()) { //if it's a new group
  37                                 seqsPerGroup[seqGroup] = 1;
  38                         }else {//it's a group we already have
  39                                 seqsPerGroup[seqGroup]++;
  40                         }
  41
  42                         gobble(fileHandle);
  43                 }
  44                 fileHandle.close();
  45 }
  46 /************************************************************/
  47 void TreeMap::removeSeq(string seqName) {
  48
  49         //erase name from namesOfSeqs
  50         for (int i = 0; i < namesOfSeqs.size(); i++) {
  51                 if (namesOfSeqs[i] == seqName)  {
  52                         namesOfSeqs.erase(namesOfSeqs.begin()+i);
  53                         break;
  54                 }
  55         }
  56
  57         //decrement sequences in this group
  58         string group = treemap[seqName].groupname;
  59         seqsPerGroup[group]--;
  60
  61         //remove seq from treemap
  62         it = treemap.find(seqName);
  63         treemap.erase(it);
  64 }
  65 /************************************************************/
  66
  67 int TreeMap::getNumGroups() {
  68
  69         return namesOfGroups.size();
  70
  71 }
  72 /************************************************************/
  73
  74 int TreeMap::getNumSeqs() {
  75
  76         return namesOfSeqs.size();
  77
  78 }
  79
  80 /************************************************************/
  81
  82 string TreeMap::getGroup(string sequenceName) {
  83
  84         it = treemap.find(sequenceName);
  85         if (it != treemap.end()) { //sequence name was in group file
  86                 return it->second.groupname;
  87         }else {
  88                 return "not found";
  89         }
  90
  91 }
  92 /************************************************************/
  93 void TreeMap::setIndex(string seq, int index) {
  94         it = treemap.find(seq);
  95         if (it != treemap.end()) { //sequence name was in group file
  96                 treemap[seq].vectorIndex = index;
  97         }else {
  98                 treemap[seq].vectorIndex = index;
  99                 treemap[seq].groupname = "not found";
 100         }
 101 }
 102 /************************************************************/
 103 int TreeMap::getIndex(string seq) {
 104
 105         it = treemap.find(seq);
 106         // if it is a valid sequence name then return index
 107         if (it != treemap.end()) { return treemap[seq].vectorIndex; }
 108         // if not return error code
 109         else { return -1; }
 110
 111 }
 112 /************************************************************/
 113
 114 void TreeMap::setNamesOfGroups(string seqGroup) {
 115                         int i, count;
 116                         count = 0;
 117                         for (i=0; i<namesOfGroups.size(); i++) {
 118                                 if (namesOfGroups[i] != seqGroup) {
 119                                         count++; //you have not found this group
 120                                 }else {
 121                                         break; //you already have it
 122                                 }
 123                         }
 124                         if (count == namesOfGroups.size()) {
 125                                 namesOfGroups.push_back(seqGroup); //new group
 126                         }
 127 }
 128 /************************************************************/
 129 bool TreeMap::isValidGroup(string groupname) {
 130         try {
 131                 for (int i = 0; i < namesOfGroups.size(); i++) {
 132                         if (groupname == namesOfGroups[i]) { return true; }
 133                 }
 134
 135                 return false;
 136         }
 137         catch(exception& e) {
 138                 m->errorOut(e, "TreeMap", "isValidGroup");
 139                 exit(1);
 140         }
 141 }
 142 /***********************************************************************/
 143
 144 void TreeMap::print(ostream& output){
 145         try {
 146
 147                 for(it = treemap.begin(); it != treemap.end(); it++){
 148                         output << it->first << '\t' << it->second.groupname << '\t' << it->second.vectorIndex << endl;
 149                 }
 150         }
 151         catch(exception& e) {
 152                 m->errorOut(e, "TreeMap", "print");
 153                 exit(1);
 154         }
 155 }
 156
 157 /************************************************************/
 158 void TreeMap::makeSim(GroupMap* groupmap) {
 159         try {
 160                 //set names of groups
 161                 namesOfGroups = groupmap->namesOfGroups;
 162
 163                 //set names of seqs to names of groups
 164                 namesOfSeqs = groupmap->namesOfGroups;
 165
 166                 // make map where key and value are both the group name since that what the tree.shared command wants
 167                 for (int i = 0; i < namesOfGroups.size(); i++) {
 168                         treemap[namesOfGroups[i]].groupname = namesOfGroups[i];
 169                         seqsPerGroup[namesOfGroups[i]] = 1;
 170                 }
 171
 172                 numGroups = namesOfGroups.size();
 173
 174         }
 175         catch(exception& e) {
 176                 m->errorOut(e, "TreeMap", "makeSim");
 177                 exit(1);
 178         }
 179 }
 180 /************************************************************/
 181 void TreeMap::makeSim(ListVector* list) {
 182         try {
 183                 //set names of groups
 184                 namesOfGroups.clear();
 185                 for(int i = 0; i < list->size(); i++) {
 186                         namesOfGroups.push_back(list->get(i));
 187                 }
 188
 189                 //set names of seqs to names of groups
 190                 namesOfSeqs = namesOfGroups;
 191
 192                 // make map where key and value are both the group name since that what the tree.shared command wants
 193                 for (int i = 0; i < namesOfGroups.size(); i++) {
 194                         treemap[namesOfGroups[i]].groupname = namesOfGroups[i];
 195                         seqsPerGroup[namesOfGroups[i]] = 1;
 196                 }
 197
 198                 numGroups = namesOfGroups.size();
 199
 200         }
 201         catch(exception& e) {
 202                 m->errorOut(e, "TreeMap", "makeSim");
 203                 exit(1);
 204         }
 205 }
 206
 207 /************************************************************/
 208