X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=decalc.cpp;h=3b3740bcea6682e14b21300a48e07fdb9f7079a3;hb=1cf188b912d6da8f2cd03dd71cecef664a699c1a;hp=def8097745a576681717c7443340d9af5bb62d81;hpb=8c1196586860f830fc9c813f2a79abab7434dc4b;p=mothur.git

diff --git a/decalc.cpp b/decalc.cpp
index def8097..3b3740b 100644
--- a/decalc.cpp
+++ b/decalc.cpp
@@ -12,7 +12,7 @@
 #include "dist.h"
 #include "eachgapdist.h"
 #include "ignoregaps.h"
-#include "eachgapdistignorens.h"
+#include "eachgapdist.h"
 
 //***************************************************************************************************************
 void DeCalculator::setMask(string ms) { 
@@ -683,7 +683,7 @@ float DeCalculator::getCoef(vector<float> obs, vector<float> qav) {
 }
 //***************************************************************************************************************
 //gets closest matches to each end, since chimeras will most likely have different parents on each end
-vector<Sequence*> DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*>& thisTemplate, vector<Sequence*>& thisFilteredTemplate, int& numWanted) {
+vector<Sequence*> DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*>& thisTemplate, vector<Sequence*>& thisFilteredTemplate, int numWanted, int minSim) {
 	try {
 		//indexes.clear();
 		
@@ -692,7 +692,7 @@ vector<Sequence*> DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*
 		vector<SeqDist> distsLeft;
 		vector<SeqDist> distsRight;
 		
-		Dist* distcalculator = new eachGapDistIgnoreNs();
+		Dist* distcalculator = new eachGapDist();
 		
 		string queryUnAligned = querySeq->getUnaligned();
 		int numBases = int(queryUnAligned.length() * 0.33);
@@ -790,6 +790,9 @@ vector<Sequence*> DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*
 		float lastLeft = distsLeft[0].dist;
 		//int lasti = 0;
 		for (int i = 0; i < numWanted+1; i++) {
+			
+			if (m->control_pressed) { return seqsMatches; }
+			
 			//add left if you havent already
 			it = seen.find(thisTemplate[distsLeft[i].index]->getName());
 			if (it == seen.end()) {  
@@ -810,14 +813,32 @@ vector<Sequence*> DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*
 			
 		}
 		
+		//are we still above the minimum similarity cutoff
+		if ((lastLeft >= minSim) || (lastRight >= minSim)) {
+			//add in ties from left
+			int i = numWanted;
+			while (i < distsLeft.size()) {  
+				if (distsLeft[i].dist == lastLeft) {  dists.push_back(distsLeft[i]);  }
+				else { break; }
+				i++;
+			}
+			
+			//add in ties from right
+			i = numWanted;
+			while (i < distsRight.size()) {  
+				if (distsRight[i].dist == lastRight) {  dists.push_back(distsRight[i]);  }
+				else { break; }
+				i++;
+			}
+		}
+		
 
-		//numWanted = dists.size();
 
 		//cout << numWanted << endl;
 		for (int i = 0; i < dists.size(); i++) {
 //			cout << db[dists[i].index]->getName() << '\t' << dists[i].dist << endl;
 
-			if (thisTemplate[dists[i].index]->getName() != querySeq->getName()) {
+			if ((thisTemplate[dists[i].index]->getName() != querySeq->getName()) && (dists[i].dist >= minSim)) {
 				Sequence* temp = new Sequence(thisTemplate[dists[i].index]->getName(), thisTemplate[dists[i].index]->getAligned()); //have to make a copy so you can trim and filter without stepping on eachother.
 			
 				seqsMatches.push_back(temp);
@@ -838,7 +859,7 @@ Sequence* DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*> db) {
 		
 		Sequence* seqsMatch;  
 		
-		Dist* distcalculator = new eachGapDistIgnoreNs();
+		Dist* distcalculator = new eachGapDist();
 		int index = 0;
 		int smallest = 1000000;