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 /************************************************************/
  68
  69 int TreeMap::getNumGroups() {
  70
  71         return namesOfGroups.size();
  72
  73 }
  74 /************************************************************/
  75
  76 int TreeMap::getNumSeqs() {
  77
  78         return namesOfSeqs.size();
  79
  80 }
  81
  82 /************************************************************/
  83
  84 string TreeMap::getGroup(string sequenceName) {
  85
  86         it = treemap.find(sequenceName);
  87         if (it != treemap.end()) { //sequence name was in group file
  88                 return it->second.groupname;
  89         }else {
  90                 return "not found";
  91         }
  92
  93 }
  94 /************************************************************/
  95 void TreeMap::setIndex(string seq, int index) {
  96         it = treemap.find(seq);
  97         if (it != treemap.end()) { //sequence name was in group file
  98                 treemap[seq].vectorIndex = index;
  99         }else {
 100                 treemap[seq].vectorIndex = index;
 101                 treemap[seq].groupname = "not found";
 102         }
 103 }
 104 /************************************************************/
 105 int TreeMap::getIndex(string seq) {
 106
 107         it = treemap.find(seq);
 108         // if it is a valid sequence name then return index
 109         if (it != treemap.end()) { return treemap[seq].vectorIndex; }
 110         // if not return error code
 111         else { return -1; }
 112
 113 }
 114 /************************************************************/
 115
 116 void TreeMap::setNamesOfGroups(string seqGroup) {
 117                         int i, count;
 118                         count = 0;
 119                         for (i=0; i<namesOfGroups.size(); i++) {
 120                                 if (namesOfGroups[i] != seqGroup) {
 121                                         count++; //you have not found this group
 122                                 }else {
 123                                         break; //you already have it
 124                                 }
 125                         }
 126                         if (count == namesOfGroups.size()) {
 127                                 namesOfGroups.push_back(seqGroup); //new group
 128                         }
 129 }
 130 /************************************************************/
 131 bool TreeMap::isValidGroup(string groupname) {
 132         try {
 133                 for (int i = 0; i < namesOfGroups.size(); i++) {
 134                         if (groupname == namesOfGroups[i]) { return true; }
 135                 }
 136
 137                 return false;
 138         }
 139         catch(exception& e) {
 140                 errorOut(e, "TreeMap", "isValidGroup");
 141                 exit(1);
 142         }
 143 }
 144 /***********************************************************************/
 145
 146 void TreeMap::print(ostream& output){
 147         try {
 148
 149                 for(it = treemap.begin(); it != treemap.end(); it++){
 150                         output << it->first << '\t' << it->second.groupname << '\t' << it->second.vectorIndex << endl;
 151                 }
 152         }
 153         catch(exception& e) {
 154                 errorOut(e, "TreeMap", "print");
 155                 exit(1);
 156         }
 157 }
 158
 159 /************************************************************/
 160 void TreeMap::makeSim(GroupMap* groupmap) {
 161         try {
 162                 //set names of groups
 163                 namesOfGroups = groupmap->namesOfGroups;
 164
 165                 //set names of seqs to names of groups
 166                 namesOfSeqs = groupmap->namesOfGroups;
 167
 168                 // make map where key and value are both the group name since that what the tree.shared command wants
 169                 for (int i = 0; i < namesOfGroups.size(); i++) {
 170                         treemap[namesOfGroups[i]].groupname = namesOfGroups[i];
 171                         seqsPerGroup[namesOfGroups[i]] = 1;
 172                 }
 173
 174                 numGroups = namesOfGroups.size();
 175
 176         }
 177         catch(exception& e) {
 178                 errorOut(e, "TreeMap", "makeSim");
 179                 exit(1);
 180         }
 181 }
 182 /************************************************************/
 183 void TreeMap::makeSim(ListVector* list) {
 184         try {
 185                 //set names of groups
 186                 namesOfGroups.clear();
 187                 for(int i = 0; i < list->size(); i++) {
 188                         namesOfGroups.push_back(list->get(i));
 189                 }
 190
 191                 //set names of seqs to names of groups
 192                 namesOfSeqs = namesOfGroups;
 193
 194                 // make map where key and value are both the group name since that what the tree.shared command wants
 195                 for (int i = 0; i < namesOfGroups.size(); i++) {
 196                         treemap[namesOfGroups[i]].groupname = namesOfGroups[i];
 197                         seqsPerGroup[namesOfGroups[i]] = 1;
 198                 }
 199
 200                 numGroups = namesOfGroups.size();
 201
 202         }
 203         catch(exception& e) {
 204                 errorOut(e, "TreeMap", "makeSim");
 205                 exit(1);
 206         }
 207 }
 208
 209 /************************************************************/
 210