X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=maligner.cpp;h=1d5258964650cad8c2e90d39414022e7dc2f0455;hb=bd93b1a6f9fe9a6a4a7ac2e9f106e5c83a438856;hp=76689e9f11bf1ab3547ef9a33053830a7b436d14;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;p=mothur.git

diff --git a/maligner.cpp b/maligner.cpp
index 76689e9..1d52589 100644
--- a/maligner.cpp
+++ b/maligner.cpp
@@ -34,6 +34,8 @@ string Maligner::getResults(Sequence* q, DeCalculator* decalc) {
 			refSeqs = getKmerSeqs(query, numWanted); //fills indexes
 		}else { m->mothurOut("not valid search."); exit(1);  } //should never get here
 		
+		if (m->control_pressed) { return chimera;  }
+		
 		refSeqs = minCoverageFilter(refSeqs);
 
 		if (refSeqs.size() < 2)  { 
@@ -46,7 +48,8 @@ string Maligner::getResults(Sequence* q, DeCalculator* decalc) {
 
 		//fills outputResults
 		chimera = chimeraMaligner(chimeraPenalty, decalc);
-	
+		
+		if (m->control_pressed) { return chimera;  }
 				
 		//free memory
 		delete query;
@@ -77,10 +80,14 @@ string Maligner::chimeraMaligner(int chimeraPenalty, DeCalculator* decalc) {
 
 		vector< vector<score_struct> > matrix = buildScoreMatrix(query->getAligned().length(), refSeqs.size()); //builds and initializes
 		
+		if (m->control_pressed) { return chimera;  }
+		
 		fillScoreMatrix(matrix, refSeqs, chimeraPenalty);
 	
 		vector<score_struct> path = extractHighestPath(matrix);
 		
+		if (m->control_pressed) { return chimera;  }
+		
 		vector<trace_struct> trace = mapTraceRegionsToAlignment(path, refSeqs);
 	
 		if (trace.size() > 1) {		chimera = "yes";	}
@@ -95,6 +102,8 @@ string Maligner::chimeraMaligner(int chimeraPenalty, DeCalculator* decalc) {
 	
 		percentIdenticalQueryChimera = computePercentID(queryInRange, chimeraSeq);
 		
+		if (m->control_pressed) { return chimera;  }
+		
 		//save output results
 		for (int i = 0; i < trace.size(); i++) {
 			int regionStart = trace[i].col;
@@ -487,24 +496,19 @@ vector<Sequence*> Maligner::getBlastSeqs(Sequence* q, int num) {
 	try {	
 		indexes.clear();
 		vector<Sequence*> refResults;
-		//generate blastdb
-		Database* database = new BlastDB(-2.0, -1.0, matchScore, misMatchPenalty);
-		for (int i = 0; i < db.size(); i++) { 	database->addSequence(*db[i]);	}
-		database->generateDB();
-		database->setNumSeqs(db.size());
-		
+				
 		//get parts of query
 		string queryUnAligned = q->getUnaligned();
 		string leftQuery = queryUnAligned.substr(0, int(queryUnAligned.length() * 0.33)); //first 1/3 of the sequence
 		string rightQuery = queryUnAligned.substr(int(queryUnAligned.length() * 0.66)); //last 1/3 of the sequence
 
-		Sequence* queryLeft = new Sequence(q->getName(), leftQuery);
-		Sequence* queryRight = new Sequence(q->getName(), rightQuery);
-		
-		vector<int> tempIndexesRight = database->findClosestMegaBlast(queryRight, num+1);
-		vector<int> tempIndexesLeft = database->findClosestMegaBlast(queryLeft, num+1);
+		Sequence* queryLeft = new Sequence(q->getName()+"left", leftQuery);
+		Sequence* queryRight = new Sequence(q->getName()+"right", rightQuery);
 		
-		//if ((tempIndexesRight.size() != (num+1)) || (tempIndexesLeft.size() != (num+1)))  {  m->mothurOut("megablast returned " + toString(tempIndexesRight.size()) + " results for the right end, and " + toString(tempIndexesLeft.size()) + " for the left end. Needed " + toString(num+1) + ". Unable to porcess sequence " + q->getName()); m->mothurOutEndLine(); return refResults; }
+		vector<int> tempIndexesRight = databaseLeft->findClosestMegaBlast(queryRight, num+1);
+		vector<int> tempIndexesLeft = databaseLeft->findClosestMegaBlast(queryLeft, num+1);
+			
+		//if ((tempIndexesRight.size() == 0) && (tempIndexesLeft.size() == 0))  {  m->mothurOut("megablast returned " + toString(tempIndexesRight.size()) + " results for the right end, and " + toString(tempIndexesLeft.size()) + " for the left end. Needed " + toString(num+1) + ". Unable to process sequence " + q->getName()); m->mothurOutEndLine(); return refResults; }
 		
 		vector<int> smaller;
 		vector<int> larger;
@@ -555,8 +559,7 @@ vector<Sequence*> Maligner::getBlastSeqs(Sequence* q, int num) {
 //cout << endl;		
 		delete queryRight;
 		delete queryLeft;
-		delete database;
-		
+			
 		return refResults;
 	}
 	catch(exception& e) {