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[mothur.git] / gotohoverlap.cpp

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+/*
+ *  gotohoverlap.cpp
+ *  
+ *
+ *  Created by Pat Schloss on 12/15/08.
+ *  Copyright 2008 Patrick D. Schloss. All rights reserved.
+ *
+ *     This class is an Alignment child class that implements the Gotoh pairwise alignment algorithm as described in:
+ *             
+ *             Gotoh O. 1982.  An improved algorithm for matching biological sequences.  J. Mol. Biol.  162:705-8.
+ *             Myers, EW & Miller, W.  1988.  Optimal alignments in linear space.  Comput Appl Biosci. 4:11-7.
+ *
+ *     This method is nice because it allows for an affine gap penalty to be assessed, which is analogous to what is used
+ *     in blast and is an alternative to Needleman-Wunsch, which only charges the same penalty for each gap position.
+ *     Because this method typically has problems at the ends when two sequences do not full overlap, we employ a separate
+ *     method to fix the ends (see Overlap class documentation)
+ *
+ */
+
+
+#include "alignmentcell.hpp"
+#include "overlap.hpp"
+#include "alignment.hpp"
+#include "gotohoverlap.hpp"
+
+/**************************************************************************************************/
+
+GotohOverlap::GotohOverlap(float gO, float gE, float f, float mm, int r) :
+       gapOpen(gO), gapExtend(gE), match(f), mismatch(mm), Alignment(r) {
+       
+       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;
+               }
+               
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GotohOverlap", "GotohOverlap");
+               exit(1);
+       }
+}
+
+/**************************************************************************************************/
+
+void GotohOverlap::align(string A, string B){
+       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{
+                                       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);
+       }
+}
+
+/**************************************************************************************************/