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
  48 int TreeMap::getNumGroups() {
  49
  50         return namesOfGroups.size();
  51
  52 }
  53 /************************************************************/
  54
  55 int TreeMap::getNumSeqs() {
  56
  57         return namesOfSeqs.size();
  58
  59 }
  60
  61 /************************************************************/
  62
  63 string TreeMap::getGroup(string sequenceName) {
  64
  65         it = treemap.find(sequenceName);
  66         if (it != treemap.end()) { //sequence name was in group file
  67                 return it->second.groupname;
  68         }else {
  69                 return "not found";
  70         }
  71
  72 }
  73 /************************************************************/
  74 void TreeMap::setIndex(string seq, int index) {
  75         it = treemap.find(seq);
  76         if (it != treemap.end()) { //sequence name was in group file
  77                 treemap[seq].vectorIndex = index;
  78         }else {
  79                 treemap[seq].vectorIndex = index;
  80                 treemap[seq].groupname = "not found";
  81         }
  82 }
  83 /************************************************************/
  84 int TreeMap::getIndex(string seq) {
  85
  86         it = treemap.find(seq);
  87         // if it is a valid sequence name then return index
  88         if (it != treemap.end()) { return treemap[seq].vectorIndex; }
  89         // if not return error code
  90         else { return -1; }
  91
  92 }
  93 /************************************************************/
  94
  95 void TreeMap::setNamesOfGroups(string seqGroup) {
  96                         int i, count;
  97                         count = 0;
  98                         for (i=0; i<namesOfGroups.size(); i++) {
  99                                 if (namesOfGroups[i] != seqGroup) {
 100                                         count++; //you have not found this group
 101                                 }else {
 102                                         break; //you already have it
 103                                 }
 104                         }
 105                         if (count == namesOfGroups.size()) {
 106                                 namesOfGroups.push_back(seqGroup); //new group
 107                         }
 108 }
 109 /************************************************************/
 110 bool TreeMap::isValidGroup(string groupname) {
 111         try {
 112                 for (int i = 0; i < namesOfGroups.size(); i++) {
 113                         if (groupname == namesOfGroups[i]) { return true; }
 114                 }
 115
 116                 return false;
 117         }
 118         catch(exception& e) {
 119                 cout << "Standard Error: " << e.what() << " has occurred in the TreeMap class Function isValidGroup. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 120                 exit(1);
 121         }
 122         catch(...) {
 123                 cout << "An unknown error has occurred in the TreeMap class function isValidGroup. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 124                 exit(1);
 125         }
 126 }
 127 /***********************************************************************/
 128
 129 void TreeMap::print(ostream& output){
 130         try {
 131
 132                 for(it = treemap.begin(); it != treemap.end(); it++){
 133                         output << it->first << '\t' << it->second.groupname << '\t' << it->second.vectorIndex << endl;
 134                 }
 135         }
 136         catch(exception& e) {
 137                 cout << "Standard Error: " << e.what() << " has occurred in the TreeMap class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 138                 exit(1);
 139         }
 140         catch(...) {
 141                 cout << "An unknown error has occurred in the TreeMap class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 142                 exit(1);
 143         }
 144 }
 145
 146 /************************************************************/
 147 void TreeMap::makeSim(GroupMap* groupmap) {
 148         try {
 149                 //set names of groups
 150                 namesOfGroups = groupmap->namesOfGroups;
 151
 152                 //set names of seqs to names of groups
 153                 namesOfSeqs = groupmap->namesOfGroups;
 154
 155                 // make map where key and value are both the group name since that what the tree.shared command wants
 156                 for (int i = 0; i < namesOfGroups.size(); i++) {
 157                         treemap[namesOfGroups[i]].groupname = namesOfGroups[i];
 158                         seqsPerGroup[namesOfGroups[i]] = 1;
 159                 }
 160
 161                 numGroups = namesOfGroups.size();
 162
 163         }
 164         catch(exception& e) {
 165                 cout << "Standard Error: " << e.what() << " has occurred in the TreeMap class Function makeSim. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 166                 exit(1);
 167         }
 168         catch(...) {
 169                 cout << "An unknown error has occurred in the TreeMap class function makeSim. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 170                 exit(1);
 171         }
 172 }
 173 /************************************************************/
 174 void TreeMap::makeSim(ListVector* list) {
 175         try {
 176                 //set names of groups
 177                 namesOfGroups.clear();
 178                 for(int i = 0; i < list->size(); i++) {
 179                         namesOfGroups.push_back(list->get(i));
 180                 }
 181
 182                 //set names of seqs to names of groups
 183                 namesOfSeqs = namesOfGroups;
 184
 185                 // make map where key and value are both the group name since that what the tree.shared command wants
 186                 for (int i = 0; i < namesOfGroups.size(); i++) {
 187                         treemap[namesOfGroups[i]].groupname = namesOfGroups[i];
 188                         seqsPerGroup[namesOfGroups[i]] = 1;
 189                 }
 190
 191                 numGroups = namesOfGroups.size();
 192
 193         }
 194         catch(exception& e) {
 195                 cout << "Standard Error: " << e.what() << " has occurred in the TreeMap class Function makeSim. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 196                 exit(1);
 197         }
 198         catch(...) {
 199                 cout << "An unknown error has occurred in the TreeMap class function makeSim. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 200                 exit(1);
 201         }
 202 }
 203
 204 /************************************************************/
 205