X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=distancedb.cpp;fp=distancedb.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=27e278574493c89d0197d99cbe71c0c3dd03d0d9;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/distancedb.cpp b/distancedb.cpp
deleted file mode 100644
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);
-	}	
-}
-
-/**************************************************************************************************/