X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=distancedb.cpp;h=27e278574493c89d0197d99cbe71c0c3dd03d0d9;hp=5c49a936e9293c629e05ea5565f334a43e5cc37c;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=6de5adaae66b28aa60a75f123005cede410c156c

diff --git a/distancedb.cpp b/distancedb.cpp
index 5c49a93..27e2785 100644
--- a/distancedb.cpp
+++ b/distancedb.cpp
@@ -11,14 +11,15 @@
 #include "database.hpp"
 #include "sequence.hpp"
 #include "distancedb.hpp"
-#include "eachgapdist.h"
+#include "onegapignore.h"
+
 
 /**************************************************************************************************/
-DistanceDB::DistanceDB() { 
+DistanceDB::DistanceDB() : Database() { 
 	try {
 		templateAligned = true;  
 		templateSeqsLength = 0; 
-		distCalculator = new eachGapDist();
+		distCalculator = new oneGapIgnoreTermGapDist();
 	}
 	catch(exception& e) {
 		m->errorOut(e, "DistanceDB", "DistanceDB");
@@ -29,7 +30,11 @@ DistanceDB::DistanceDB() {
 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 (!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(); }
 				
@@ -45,34 +50,68 @@ void DistanceDB::addSequence(Sequence seq) {
 vector<int> DistanceDB::findClosestSequences(Sequence* query, int numWanted){
 	try {
 		vector<int> topMatches;
+		Scores.clear();
 		bool templateSameLength = true;
 		string sequence = query->getAligned();
-		vector<seqDist> dists;
+		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 (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) {
-			//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();
+			if (numWanted != 1) {
 				
-				//save distance to each template sequence
-				seqDist temp(-1, i, dist);
-				dists.push_back(temp);
-			}
-			
-			sort(dists.begin(), dists.end(), compareSequenceDistance);  //sorts by distance lowest to highest
-			
-			//fill topmatches with numwanted closest sequences indexes
-			for (int i = 0; i < numWanted; i++) {
-				topMatches.push_back(dists[i].seq2);
+				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();
+			m->mothurOut("cannot find closest matches using distance method for " + query->getName() + " without aligned template sequences of the same length.");
+			m->mothurOutEndLine();
 			exit(1);
 		}