X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=gotohoverlap.cpp;h=ea27df07068a5e2060d3a1be4220a9b2de57822c;hp=57d884bf5f17a1d00a524c52997dac751f47fe81;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=526a868606faa50caf86e7399f7554c0335b39e5

diff --git a/gotohoverlap.cpp b/gotohoverlap.cpp
index 57d884b..ea27df0 100644
--- a/gotohoverlap.cpp
+++ b/gotohoverlap.cpp
@@ -17,7 +17,6 @@
  *
  */
 
-using namespace std;
 
 #include "alignmentcell.hpp"
 #include "overlap.hpp"
@@ -26,65 +25,78 @@ using namespace std;
 
 /**************************************************************************************************/
 
-GotohOverlap::GotohOverlap(float gO, float gE, float m, float mm, int r) :
-	gapOpen(gO), gapExtend(gE), match(m), mismatch(mm), Alignment(r) {
+GotohOverlap::GotohOverlap(float gO, float gE, float f, float mm, int r) :
+	gapOpen(gO), gapExtend(gE), match(f), mismatch(mm), Alignment(r) {
 	
-	for(int i=1;i<nCols;i++){				//	we initialize the dynamic programming matrix by setting the pointers in
-		alignment[0][i].prevCell = 'l';		//	the first row to the left
-		alignment[0][i].cValue = 0;
-		alignment[0][i].dValue = 0;
+	try {
+		for(int i=1;i<nCols;i++){				//	we initialize the dynamic programming matrix by setting the pointers in
+			alignment[0][i].prevCell = 'l';		//	the first row to the left
+			alignment[0][i].cValue = 0;
+			alignment[0][i].dValue = 0;
+		}
+		
+		for(int i=1;i<nRows;i++){				//	we initialize the dynamic programming matrix by setting the pointers in
+			alignment[i][0].prevCell = 'u';		//	the first column upward
+			alignment[i][0].cValue = 0;
+			alignment[i][0].iValue = 0;
+		}
+		
 	}
-	
-	for(int i=1;i<nRows;i++){				//	we initialize the dynamic programming matrix by setting the pointers in
-		alignment[i][0].prevCell = 'u';		//	the first column upward
-		alignment[i][0].cValue = 0;
-		alignment[i][0].iValue = 0;
+	catch(exception& e) {
+		m->errorOut(e, "GotohOverlap", "GotohOverlap");
+		exit(1);
 	}
 }
 
 /**************************************************************************************************/
 
 void GotohOverlap::align(string A, string B){
-	
-	seqA = ' ' + A;	lA = seqA.length();		//	the algorithm requires that the first character be a dummy value
-	seqB = ' ' + B;	lB = seqB.length();		//	the algorithm requires that the first character be a dummy value
-	
-	for(int i=1;i<lB;i++){					//	the recursion here is shown in Webb and Miller, Fig. 1A.  Note that 
-		for(int j=1;j<lA;j++){				//	if we need to conserve on space we should see Fig. 1B, which is linear
-											//	in space, which I think is unnecessary
-			float diagonal;
-			if(seqB[i] == seqA[j])	{	diagonal = alignment[i-1][j-1].cValue + match;		}
-			else					{	diagonal = alignment[i-1][j-1].cValue + mismatch;	}
-			
-			alignment[i][j].iValue = max(alignment[i][j-1].iValue, alignment[i][j-1].cValue + gapOpen) + gapExtend;
-			alignment[i][j].dValue = max(alignment[i-1][j].dValue, alignment[i-1][j].cValue + gapOpen) + gapExtend;
-			
-			if(alignment[i][j].iValue > alignment[i][j].dValue){
-				if(alignment[i][j].iValue > diagonal){
-					alignment[i][j].cValue = alignment[i][j].iValue;
-					alignment[i][j].prevCell = 'l';
+	try {
+		seqA = ' ' + A;	lA = seqA.length();		//	the algorithm requires that the first character be a dummy value
+		seqB = ' ' + B;	lB = seqB.length();		//	the algorithm requires that the first character be a dummy value
+		
+		for(int i=1;i<lB;i++){					//	the recursion here is shown in Webb and Miller, Fig. 1A.  Note that 
+			for(int j=1;j<lA;j++){				//	if we need to conserve on space we should see Fig. 1B, which is linear
+				//	in space, which I think is unnecessary
+				float diagonal;
+				if(seqB[i] == seqA[j])	{	diagonal = alignment[i-1][j-1].cValue + match;		}
+				else					{	diagonal = alignment[i-1][j-1].cValue + mismatch;	}
+				
+				alignment[i][j].iValue = max(alignment[i][j-1].iValue, alignment[i][j-1].cValue + gapOpen) + gapExtend;
+				alignment[i][j].dValue = max(alignment[i-1][j].dValue, alignment[i-1][j].cValue + gapOpen) + gapExtend;
+				
+				if(alignment[i][j].iValue > alignment[i][j].dValue){
+					if(alignment[i][j].iValue > diagonal){
+						alignment[i][j].cValue = alignment[i][j].iValue;
+						alignment[i][j].prevCell = 'l';
+					}
+					else{
+						alignment[i][j].cValue = diagonal;
+						alignment[i][j].prevCell = 'd';
+					}
 				}
 				else{
-					alignment[i][j].cValue = diagonal;
-					alignment[i][j].prevCell = 'd';
+					if(alignment[i][j].dValue > diagonal){
+						alignment[i][j].cValue = alignment[i][j].dValue;
+						alignment[i][j].prevCell = 'u';
+					}
+					else{
+						alignment[i][j].cValue = diagonal;
+						alignment[i][j].prevCell = 'd';
+					}
 				}
+				
 			}
-			else{
-				if(alignment[i][j].dValue > diagonal){
-					alignment[i][j].cValue = alignment[i][j].dValue;
-					alignment[i][j].prevCell = 'u';
-				}
-				else{
-					alignment[i][j].cValue = diagonal;
-					alignment[i][j].prevCell = 'd';
-				}
-			}
-			
 		}
+		Overlap over;
+		over.setOverlap(alignment, lA, lB, 0);	//	Fix the gaps at the ends of the sequences
+		traceBack();							//	Construct the alignment and set seqAaln and seqBaln
+		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GotohOverlap", "align");
+		exit(1);
 	}
-	Overlap over;
-	over.setOverlap(alignment, lA, lB, 0);	//	Fix the gaps at the ends of the sequences
-	traceBack();							//	Construct the alignment and set seqAaln and seqBaln
 }
 
 /**************************************************************************************************/