moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / distancedb.cpp

diff --git a/distancedb.cpp b/distancedb.cpp
deleted file mode 100644 (file)
index 27e2785..0000000
--- a/distancedb.cpp
+++ /dev/null
@@ -1,145 +0,0 @@
-/*
- *  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);
-       }       
-}
-
-/**************************************************************************************************/