X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=overlap.cpp;fp=overlap.cpp;h=9645e7a748ce72417f8c8bcbd272ac38dde1aca4;hb=526a868606faa50caf86e7399f7554c0335b39e5;hp=0000000000000000000000000000000000000000;hpb=c35f02a218ce8f430a75850b4d9fabb96b3a022b;p=mothur.git

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+/*
+ *  overlap.cpp
+ *  
+ *
+ *  Created by Pat Schloss on 12/15/08.
+ *  Copyright 2008 Patrick D. Schloss. All rights reserved.
+ *
+ *	This class cleans up the alignment at the 3' end of the alignments.  Because the Gotoh and Needleman-Wunsch
+ *	algorithms start the traceback from the lower-right corner of the dynamic programming matrix, there may be a lot of
+ *	scattered bases in the alignment near the 3' end of the alignment.  Here we basically look for the largest score
+ *	in the last column and row to determine whether there should be exta gaps in sequence A or sequence B.  The gap
+ *	issues at the 5' end of the alignment seem to take care of themselves in the traceback.
+ *
+ */
+using namespace std;
+
+#include "alignmentcell.hpp"
+#include "overlap.hpp"
+
+
+/**************************************************************************************************/
+
+int Overlap::maxRow(vector<vector<AlignmentCell> >& alignment, const int band){
+	
+	float max = -100;
+	int end = lA - 1;
+	int index = end;
+	
+	for(int i=band;i<lB;i++){					//	find the row where the right most column has the highest alignment
+		if(alignment[i][end].cValue >= max){	//	score.
+			index = i;
+			max = alignment[i][end].cValue;
+		}
+	}
+	return index;
+}
+
+/**************************************************************************************************/
+
+int Overlap::maxColumn(vector<vector<AlignmentCell> >& alignment, const int band){
+	
+	float max = -100;
+	int end = lB - 1;
+	int index = end;
+	
+	for(int i=band;i<lA;i++){					//	find the column where the bottom most column has the highest
+		if(alignment[end][i].cValue >= max){	//	alignment score.
+			index = i;
+			max = alignment[end][i].cValue;
+		}
+	}
+	return index;
+}
+
+/**************************************************************************************************/
+
+void Overlap::setOverlap(vector<vector<AlignmentCell> >& alignment, const int nA, const int nB, const int band=0){
+	
+	lA = nA;
+	lB = nB;	
+	
+	int rowIndex = maxRow(alignment, band);		//	get the index for the row with the highest right hand side score
+	int colIndex = maxColumn(alignment, band);	//	get the index for the column with the highest bottom row score
+	
+	int row = lB-1;
+	int column = lA-1;
+	
+	if(colIndex == column && rowIndex == row){}	//	if the max values are the lower right corner, then we're good
+	else if(alignment[row][colIndex].cValue < alignment[rowIndex][column].cValue){
+		for(int i=rowIndex+1;i<lB;i++){			//	decide whether sequence A or B needs the gaps at the end either set 
+			alignment[i][column].prevCell = 'u';//	the pointer upwards or...
+		}
+		
+	}
+	else {
+		for(int i=colIndex+1;i<lA;i++){
+			alignment[row][i].prevCell = 'l';	//	...to the left
+		}
+	}
+}												//	the traceback should take care of the gaps at the 5' end
+
+/**************************************************************************************************/
+