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[mothur.git] / overlap.cpp

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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.
+ *
+ */
+
+#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
+
+/**************************************************************************************************/
+