moving source to source folder

[mothur.git] / source / distancedb.cpp

diff --git a/source/distancedb.cpp b/source/distancedb.cpp
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+++ b/source/distancedb.cpp
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+/*
+ *  distancedb.cpp
+ *  
+ *
+ *  Created by Pat Schloss on 12/29/08.
+ *  Copyright 2008 Patrick D. Schloss. All rights reserved.
+ *
+ */
+
+
+#include "database.hpp"
+#include "sequence.hpp"
+#include "distancedb.hpp"
+#include "onegapignore.h"
+
+
+/**************************************************************************************************/
+DistanceDB::DistanceDB() : Database() { 
+       try {
+               templateAligned = true;  
+               templateSeqsLength = 0; 
+               distCalculator = new oneGapIgnoreTermGapDist();
+       }
+       catch(exception& e) {
+               m->errorOut(e, "DistanceDB", "DistanceDB");
+               exit(1);
+       }       
+}
+/**************************************************************************************************/
+void DistanceDB::addSequence(Sequence seq) {
+       try {
+               //are the template sequences aligned
+               if (!isAligned(seq.getAligned())) {
+                       templateAligned = false;
+                       m->mothurOut(seq.getName() + " is not aligned. Sequences must be aligned to use the distance method.");
+                       m->mothurOutEndLine(); 
+               }
+               
+               if (templateSeqsLength == 0) { templateSeqsLength = seq.getAligned().length(); }
+                               
+               data.push_back(seq);
+       }
+       catch(exception& e) {
+               m->errorOut(e, "DistanceDB", "addSequence");
+               exit(1);
+       }       
+}
+/**************************************************************************************************/
+//returns indexes to top matches
+vector<int> DistanceDB::findClosestSequences(Sequence* query, int numWanted){
+       try {
+               vector<int> topMatches;
+               Scores.clear();
+               bool templateSameLength = true;
+               string sequence = query->getAligned();
+               vector<seqDist> dists; 
+               
+               searchScore = -1.0;
+       
+               if (numWanted > data.size()){
+                       m->mothurOut("numwanted is larger than the number of template sequences, using "+ toString(data.size()) + ".");
+                       m->mothurOutEndLine();
+                       numWanted = data.size();
+               }
+               
+               if (sequence.length() != templateSeqsLength) { templateSameLength = false; }
+               
+               if (templateSameLength && templateAligned) {
+                       if (numWanted != 1) {
+                               
+                               dists.resize(data.size());
+                               
+                               //calc distance from this sequence to every sequence in the template
+                               for (int i = 0; i < data.size(); i++) {
+                                       distCalculator->calcDist(*query, data[i]);
+                                       float dist = distCalculator->getDist();
+                                       
+                                       //save distance to each template sequence
+                                       dists[i].seq1 = -1;
+                                       dists[i].seq2 = i;
+                                       dists[i].dist = dist;
+                               }
+                               
+                               sort(dists.begin(), dists.end(), compareSequenceDistance);  //sorts by distance lowest to highest
+                               
+                               //save distance of best match
+                               searchScore = dists[0].dist;
+                               
+                               //fill topmatches with numwanted closest sequences indexes
+                               for (int i = 0; i < numWanted; i++) {
+                                       topMatches.push_back(dists[i].seq2);
+                                       Scores.push_back(dists[i].dist);
+                               }
+                       }else {
+                               int bestIndex = 0;
+                               float smallDist = 100000;
+                               for (int i = 0; i < data.size(); i++) {
+                                       distCalculator->calcDist(*query, data[i]);
+                                       float dist = distCalculator->getDist();
+                                       
+                                       //are you smaller?
+                                       if (dist < smallDist) {
+                                               bestIndex = i;
+                                               smallDist = dist;
+                                       }
+                               }
+                               searchScore = smallDist;
+                               topMatches.push_back(bestIndex);
+                               Scores.push_back(smallDist);
+                       }
+               
+               }else{
+                       m->mothurOut("cannot find closest matches using distance method for " + query->getName() + " without aligned template sequences of the same length.");
+                       m->mothurOutEndLine();
+                       exit(1);
+               }
+               
+               return topMatches;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "DistanceDB", "findClosestSequence");
+               exit(1);
+       }       
+}
+/**************************************************************************************************/
+bool DistanceDB::isAligned(string seq){
+       try {
+               bool aligned;
+               
+               int pos = seq.find_first_of(".-");
+               
+               if (pos != seq.npos) {
+                       aligned = true;
+               }else { aligned = false; }
+               
+               
+               return aligned;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "DistanceDB", "isAligned");
+               exit(1);
+       }       
+}
+
+/**************************************************************************************************/