5 * Created by Pat Schloss on 12/29/08.
6 * Copyright 2008 Patrick D. Schloss. All rights reserved.
11 #include "database.hpp"
12 #include "sequence.hpp"
13 #include "distancedb.hpp"
14 #include "onegapignore.h"
17 /**************************************************************************************************/
18 DistanceDB::DistanceDB() : Database() {
20 templateAligned = true;
21 templateSeqsLength = 0;
22 distCalculator = new oneGapIgnoreTermGapDist();
25 m->errorOut(e, "DistanceDB", "DistanceDB");
29 /**************************************************************************************************/
30 void DistanceDB::addSequence(Sequence seq) {
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();
39 if (templateSeqsLength == 0) { templateSeqsLength = seq.getAligned().length(); }
44 m->errorOut(e, "DistanceDB", "addSequence");
48 /**************************************************************************************************/
49 //returns indexes to top matches
50 vector<int> DistanceDB::findClosestSequences(Sequence* query, int numWanted){
52 vector<int> topMatches;
54 bool templateSameLength = true;
55 string sequence = query->getAligned();
56 vector<seqDist> dists;
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();
66 if (sequence.length() != templateSeqsLength) { templateSameLength = false; }
68 if (templateSameLength && templateAligned) {
71 dists.resize(data.size());
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();
78 //save distance to each template sequence
84 sort(dists.begin(), dists.end(), compareSequenceDistance); //sorts by distance lowest to highest
86 //save distance of best match
87 searchScore = dists[0].dist;
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);
96 float smallDist = 100000;
97 for (int i = 0; i < data.size(); i++) {
98 distCalculator->calcDist(*query, data[i]);
99 float dist = distCalculator->getDist();
102 if (dist < smallDist) {
107 searchScore = smallDist;
108 topMatches.push_back(bestIndex);
109 Scores.push_back(smallDist);
113 m->mothurOut("cannot find closest matches using distance method for " + query->getName() + " without aligned template sequences of the same length.");
114 m->mothurOutEndLine();
120 catch(exception& e) {
121 m->errorOut(e, "DistanceDB", "findClosestSequence");
125 /**************************************************************************************************/
126 bool DistanceDB::isAligned(string seq){
130 int pos = seq.find_first_of(".-");
132 if (pos != seq.npos) {
134 }else { aligned = false; }
139 catch(exception& e) {
140 m->errorOut(e, "DistanceDB", "isAligned");
145 /**************************************************************************************************/