distancedb.cpp

   1 /*
   2  *  distancedb.cpp
   3  *
   4  *
   5  *  Created by Pat Schloss on 12/29/08.
   6  *  Copyright 2008 Patrick D. Schloss. All rights reserved.
   7  *
   8  */
   9
  10
  11 #include "database.hpp"
  12 #include "sequence.hpp"
  13 #include "distancedb.hpp"
  14 #include "onegapignore.h"
  15
  16
  17 /**************************************************************************************************/
  18 DistanceDB::DistanceDB() : Database() {
  19         try {
  20                 templateAligned = true;
  21                 templateSeqsLength = 0;
  22                 distCalculator = new oneGapIgnoreTermGapDist();
  23         }
  24         catch(exception& e) {
  25                 m->errorOut(e, "DistanceDB", "DistanceDB");
  26                 exit(1);
  27         }
  28 }
  29 /**************************************************************************************************/
  30 void DistanceDB::addSequence(Sequence seq) {
  31         try {
  32                 //are the template sequences aligned
  33                 if (!isAligned(seq.getAligned())) {
  34                         templateAligned = false;
  35                         m->mothurOut(seq.getName() + " is not aligned. Sequences must be aligned to use the distance method.");
  36                         m->mothurOutEndLine();
  37                 }
  38
  39                 if (templateSeqsLength == 0) { templateSeqsLength = seq.getAligned().length(); }
  40
  41                 data.push_back(seq);
  42         }
  43         catch(exception& e) {
  44                 m->errorOut(e, "DistanceDB", "addSequence");
  45                 exit(1);
  46         }
  47 }
  48 /**************************************************************************************************/
  49 //returns indexes to top matches
  50 vector<int> DistanceDB::findClosestSequences(Sequence* query, int numWanted){
  51         try {
  52                 vector<int> topMatches;
  53                 Scores.clear();
  54                 bool templateSameLength = true;
  55                 string sequence = query->getAligned();
  56                 vector<seqDist> dists;
  57
  58                 searchScore = -1.0;
  59
  60                 if (numWanted > data.size()){
  61                         m->mothurOut("numwanted is larger than the number of template sequences, using "+ toString(data.size()) + ".");
  62                         m->mothurOutEndLine();
  63                         numWanted = data.size();
  64                 }
  65
  66                 if (sequence.length() != templateSeqsLength) { templateSameLength = false; }
  67
  68                 if (templateSameLength && templateAligned) {
  69                         if (numWanted != 1) {
  70
  71                                 dists.resize(data.size());
  72
  73                                 //calc distance from this sequence to every sequence in the template
  74                                 for (int i = 0; i < data.size(); i++) {
  75                                         distCalculator->calcDist(*query, data[i]);
  76                                         float dist = distCalculator->getDist();
  77
  78                                         //save distance to each template sequence
  79                                         dists[i].seq1 = -1;
  80                                         dists[i].seq2 = i;
  81                                         dists[i].dist = dist;
  82                                 }
  83
  84                                 sort(dists.begin(), dists.end(), compareSequenceDistance);  //sorts by distance lowest to highest
  85
  86                                 //save distance of best match
  87                                 searchScore = dists[0].dist;
  88
  89                                 //fill topmatches with numwanted closest sequences indexes
  90                                 for (int i = 0; i < numWanted; i++) {
  91                                         topMatches.push_back(dists[i].seq2);
  92                                         Scores.push_back(dists[i].dist);
  93                                 }
  94                         }else {
  95                                 int bestIndex = 0;
  96                                 float smallDist = 100000;
  97                                 for (int i = 0; i < data.size(); i++) {
  98                                         distCalculator->calcDist(*query, data[i]);
  99                                         float dist = distCalculator->getDist();
 100
 101                                         //are you smaller?
 102                                         if (dist < smallDist) {
 103                                                 bestIndex = i;
 104                                                 smallDist = dist;
 105                                         }
 106                                 }
 107                                 searchScore = smallDist;
 108                                 topMatches.push_back(bestIndex);
 109                                 Scores.push_back(smallDist);
 110                         }
 111
 112                 }else{
 113                         m->mothurOut("cannot find closest matches using distance method for " + query->getName() + " without aligned template sequences of the same length.");
 114                         m->mothurOutEndLine();
 115                         exit(1);
 116                 }
 117
 118                 return topMatches;
 119         }
 120         catch(exception& e) {
 121                 m->errorOut(e, "DistanceDB", "findClosestSequence");
 122                 exit(1);
 123         }
 124 }
 125 /**************************************************************************************************/
 126 bool DistanceDB::isAligned(string seq){
 127         try {
 128                 bool aligned;
 129
 130                 int pos = seq.find_first_of(".-");
 131
 132                 if (pos != seq.npos) {
 133                         aligned = true;
 134                 }else { aligned = false; }
 135
 136
 137                 return aligned;
 138         }
 139         catch(exception& e) {
 140                 m->errorOut(e, "DistanceDB", "isAligned");
 141                 exit(1);
 142         }
 143 }
 144
 145 /**************************************************************************************************/