X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=slayer.cpp;h=5d5a48b864695ce2ed92357006b834efa24195bb;hb=3a13eff5c26d6fc156a299c9fa7f5497bded94a0;hp=66db22b6a36ae9a0f7f9dd383201cd3852a120b2;hpb=5a1e62397b91f57d0d3aff635891df04b8999a88;p=mothur.git

diff --git a/slayer.cpp b/slayer.cpp
index 66db22b..5d5a48b 100644
--- a/slayer.cpp
+++ b/slayer.cpp
@@ -11,7 +11,7 @@
 
 /***********************************************************************/
 Slayer::Slayer(int win, int increment, int parentThreshold, float div, int i, int snp) :
-		windowSize(win), windowStep(increment), parentFragmentThreshold(parentThreshold), divRThreshold(div), iters(i), percentSNPSample(snp){}
+		windowSize(win), windowStep(increment), parentFragmentThreshold(parentThreshold), divRThreshold(div), iters(i), percentSNPSample(snp){ m = MothurOut::getInstance(); }
 /***********************************************************************/
 string Slayer::getResults(Sequence* query, vector<Sequence*> refSeqs) {
 	try {
@@ -20,6 +20,8 @@ string Slayer::getResults(Sequence* query, vector<Sequence*> refSeqs) {
 		for (int i = 0; i < refSeqs.size(); i++) {
 		
 			for (int j = i+1; j < refSeqs.size(); j++) {
+			
+				if (m->control_pressed) { return "no";  }
 	
 				//make copies of query and each parent because runBellerophon removes gaps and messes them up
 				Sequence* q = new Sequence(query->getName(), query->getAligned());
@@ -29,12 +31,26 @@ string Slayer::getResults(Sequence* query, vector<Sequence*> refSeqs) {
 				map<int, int> spots;  //map from spot in original sequence to spot in filtered sequence for query and both parents
 				vector<data_struct> divs = runBellerophon(q, leftParent, rightParent, spots);
 				
+				if (m->control_pressed) { 
+					delete q;
+					delete leftParent;
+					delete rightParent;
+					return "no"; 
+				}
+				
 				vector<data_struct> selectedDivs;
 				for (int k = 0; k < divs.size(); k++) {
 				
 					vector<snps> snpsLeft = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winLStart, divs[k].winLEnd);
 					vector<snps> snpsRight = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winRStart, divs[k].winREnd);
 					
+					if (m->control_pressed) { 
+						delete q;
+						delete leftParent;
+						delete rightParent;
+						return "no"; 
+					}
+					
 					int numSNPSLeft = snpsLeft.size();
 					int numSNPSRight = snpsRight.size();
 					
@@ -54,6 +70,13 @@ string Slayer::getResults(Sequence* query, vector<Sequence*> refSeqs) {
 							
 							float BS_A, BS_B;
 							bootstrapSNPS(snpsLeft, snpsRight, BS_A, BS_B);
+							
+							if (m->control_pressed) { 
+								delete q;
+								delete leftParent;
+								delete rightParent;
+								return "no"; 
+							}
 
 							divs[k].bsa = BS_A;
 							divs[k].bsb = BS_B;
@@ -98,7 +121,7 @@ string Slayer::getResults(Sequence* query, vector<Sequence*> refSeqs) {
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "Slayer", "getResults");
+		m->errorOut(e, "Slayer", "getResults");
 		exit(1);
 	}
 }
@@ -130,12 +153,14 @@ vector<data_struct> Slayer::runBellerophon(Sequence* q, Sequence* pA, Sequence*
 	
 		//check window size
 		if (length < (2*windowSize+windowStep)) { 
-			mothurOut("Your window size is too large for " + q->getName() + ". I will make the window size " + toString(length/4) + " which is 1/4 the filtered length."); mothurOutEndLine();	
+			m->mothurOut("Your window size is too large for " + q->getName() + ". I will make the window size " + toString(length/4) + " which is 1/4 the filtered length."); m->mothurOutEndLine();	
 			windowSize = length / 4;
 		}
 		
 		for (int i = windowSize-1; i <= (length - windowSize); i += windowStep) {
 		
+			if (m->control_pressed) { return data; }
+		
 			int breakpoint = i;
 			int leftLength = breakpoint + 1;
 			int rightLength = length - leftLength;
@@ -208,7 +233,7 @@ vector<data_struct> Slayer::runBellerophon(Sequence* q, Sequence* pA, Sequence*
 		
 	}
 	catch(exception& e) {
-		errorOut(e, "Slayer", "runBellerophon");
+		m->errorOut(e, "Slayer", "runBellerophon");
 		exit(1);
 	}
 }
@@ -257,12 +282,12 @@ vector<snps> Slayer::getSNPS(string parentA, string query, string parentB, int l
 		
 	}
 	catch(exception& e) {
-		errorOut(e, "Slayer", "getSNPS");
+		m->errorOut(e, "Slayer", "getSNPS");
 		exit(1);
 	}
 }
 /***********************************************************************/
-void Slayer::bootstrapSNPS(vector<snps> left, vector<snps> right, float& BSA, float& BSB) {
+int Slayer::bootstrapSNPS(vector<snps> left, vector<snps> right, float& BSA, float& BSB) {
 	try {
 
 		srand((unsigned)time( NULL ));
@@ -276,6 +301,8 @@ void Slayer::bootstrapSNPS(vector<snps> left, vector<snps> right, float& BSA, fl
 		for (int i = 0; i < iters; i++) {
 			//random sampling with replacement.
 		
+			if (m->control_pressed) { return 0;  }
+			
 			vector<snps> selectedLeft;
 
 			for (int j = 0; j < numLeft; j++) {
@@ -339,10 +366,12 @@ void Slayer::bootstrapSNPS(vector<snps> left, vector<snps> right, float& BSA, fl
 		BSA = ((float) count_A / (float) iters) * 100;
 		BSB = ((float) count_B / (float) iters) * 100;
 //cout << "bsa = " << BSA << " bsb = " << BSB << endl;
+
+		return 0;
 	
 	}
 	catch(exception& e) {
-		errorOut(e, "Slayer", "bootstrapSNPS");
+		m->errorOut(e, "Slayer", "bootstrapSNPS");
 		exit(1);
 	}
 }
@@ -363,7 +392,7 @@ float Slayer::snpQA(vector<snps> data) {
 		return percentID;
 	}
 	catch(exception& e) {
-		errorOut(e, "Slayer", "snpQA");
+		m->errorOut(e, "Slayer", "snpQA");
 		exit(1);
 	}
 }
@@ -385,7 +414,7 @@ float Slayer::snpQB(vector<snps> data) {
 
 	}
 	catch(exception& e) {
-		errorOut(e, "Slayer", "snpQB");
+		m->errorOut(e, "Slayer", "snpQB");
 		exit(1);
 	}
 }
@@ -406,7 +435,7 @@ float Slayer::snpAB(vector<snps> data) {
 
 	}
 	catch(exception& e) {
-		errorOut(e, "Slayer", "snpAB");
+		m->errorOut(e, "Slayer", "snpAB");
 		exit(1);
 	}
 }
@@ -428,7 +457,7 @@ float Slayer::computePercentID(string queryFrag, string parent, int left, int ri
 		return percentID;
 	}
 	catch(exception& e) {
-		errorOut(e, "Slayer", "computePercentID");
+		m->errorOut(e, "Slayer", "computePercentID");
 		exit(1);
 	}
 }
@@ -494,7 +523,7 @@ map<int, int> Slayer::verticalFilter(vector<Sequence*> seqs) {
 		return maskMap;
 	}
 	catch(exception& e) {
-		errorOut(e, "Slayer", "verticalFilter");
+		m->errorOut(e, "Slayer", "verticalFilter");
 		exit(1);
 	}
 }