810 lines
31 KiB
Java
810 lines
31 KiB
Java
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package org.broadinstitute.sting.utils;
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import net.sf.samtools.CigarElement;
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import net.sf.samtools.CigarOperator;
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import net.sf.samtools.Cigar;
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import java.util.List;
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import java.util.ArrayList;
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import java.util.Collections;
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/**
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* Created by IntelliJ IDEA.
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* User: asivache
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* Date: Mar 23, 2009
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* Time: 1:54:54 PM
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* To change this template use File | Settings | File Templates.
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*/
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public class SWPairwiseAlignment {
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private String s1;
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private String s2;
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private int i1;
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private int i2;
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private int alignment_offset; // offset of s2 w/respect to s1
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private Cigar alignmentCigar;
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private double w_match;
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private double w_mismatch;
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private double w_open;
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private double w_extend;
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private int best_mm; // mismatch count
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private static final int IMPOSSIBLE = 1000000000;
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private static final int MSTATE = 0;
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private static final int ISTATE = 1;
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private static final int DSTATE = 2;
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public SWPairwiseAlignment(String seq1, String seq2, int id1, int id2, double match, double mismatch, double open, double extend ) {
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s1 = seq1;
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s2 = seq2;
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i1 = id1;
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i2 = id2;
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w_match = match;
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w_mismatch = mismatch;
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w_open = open;
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w_extend = extend;
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best_mm = IMPOSSIBLE;
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//next_mm = IMPOSSIBLE;
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align4(s1,s2);
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}
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public SWPairwiseAlignment(String seq1, String seq2, int id1, int id2) {
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this(seq1,seq2,id1,id2,1.0,-1.0/3.0,-1.0-1.0/3.0,-1.0/3.0); // match=1, mismatch = -1/3, gap=-(1+k/3)
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}
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/** Initializes the alignment with pair of sequences (that will be immediately aligned) and
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* sets their external ids to -1. Such un-annotated pairwise alignment can not be added to MultipleAlignment.
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*
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*/
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public SWPairwiseAlignment(String seq1, String seq2) {
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this(seq1,seq2,-1,-1);
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}
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public SWPairwiseAlignment(String seq1, String seq2, double match, double mismatch, double open, double extend) {
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this(seq1,seq2,-1,-1,match,mismatch,open, extend);
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}
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public Cigar getCigar() { return alignmentCigar ; }
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public int getAlignmentStart2wrt1() { return alignment_offset; }
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public void align(String a, String b) {
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int n = a.length();
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int m = b.length();
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int [][] sw = new int[n+1][m+1];
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// build smith-waterman matrix:
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for ( int i = 1 ; i < n+1 ; i++ ) {
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char a_base = Character.toUpperCase(a.charAt(i-1)); // letter in a at the current pos
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for ( int j = 1 ; j < m+1 ; j++ ) {
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char b_base = Character.toUpperCase(b.charAt(j-1)); // letter in b at the current pos
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int step_diag = sw[i-1][j-1] + w(a_base,b_base);
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int step_down = sw[i-1][j]+w(a_base,'-');
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int step_right = sw[i][j-1]+w('-',b_base);
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sw[i][j] = Math.max(0, Math.max(step_diag,Math.max(step_down,step_right)));
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}
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}
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// print(sw,a,b);
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PrimitivePair.Int p = new PrimitivePair.Int();
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int maxscore = 0;
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int segment_length = 0; // length of the segment (continuous matches, insertions or deletions)
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// look for largest score. we use >= combined with the traversal direction
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// to ensure that if two scores are equal, the one closer to diagonal gets picked
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for ( int i = 1 ; i < n+1 ; i++ ) {
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if ( sw[i][m] >= maxscore ) { p.first = i; p.second = m ; maxscore = sw[i][m]; }
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}
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for ( int j = 1 ; j < m+1 ; j++ ) {
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if ( sw[n][j] > maxscore ||
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sw[n][j] == maxscore && Math.abs(n-j) < Math.abs(p.first-p.second)) {
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p.first = n;
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p.second = j ;
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maxscore = sw[n][j];
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segment_length = m - j; // end of sequence 2 is overhanging; we will just record it as 'M' segment
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}
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}
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// System.out.println("\ni="+p.first+"; j="+p.second);
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// p holds the position we start backtracking from; we will be assembling a cigar in the backwards order
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// we will be placing all insertions and deletions into sequence b, so the state are named w/regard
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// to that sequence
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int state = MSTATE;
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int [] scores = new int[3];
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List<CigarElement> lce = new ArrayList<CigarElement>(5);
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do {
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scores[ISTATE] = sw[p.first][p.second-1]; // moving left: same base on a, prev base on b = insertion on b
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scores[DSTATE] = sw[p.first-1][p.second]; // moving up: same base on b, prev base on a = deletion on b
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scores[MSTATE] = sw[p.first-1][p.second-1]; // moving diagonal : mathc/mismatch
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int new_state = findMaxInd(scores,MSTATE);
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// move to next best location in the sw matrix:
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switch( new_state ) {
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case MSTATE: p.first--; p.second--; break;
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case ISTATE: p.second--; break;
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case DSTATE: p.first--; break;
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}
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// now let's see if the state actually changed:
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if ( new_state == state ) segment_length++;
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else {
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// state changed, lets emit previous segment, whatever it was (Insertion Deletion, or (Mis)Match).
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CigarOperator o=null;
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switch(state) {
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case MSTATE: o = CigarOperator.M; break;
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case ISTATE: o = CigarOperator.I; break;
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case DSTATE: o = CigarOperator.D; break;
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}
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CigarElement e = new CigarElement(segment_length,o);
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lce.add(e);
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segment_length = 1;
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state = new_state;
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}
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} while ( scores[state] != 0 );
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// post-process the last segment we are still keeping
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CigarOperator o=null;
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switch(state) {
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case MSTATE: o = CigarOperator.M; break;
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case ISTATE: o = CigarOperator.I; break;
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case DSTATE: o = CigarOperator.D; break;
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}
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alignment_offset = p.first - p.second;
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segment_length+=p.second;
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CigarElement e = new CigarElement(segment_length,o);
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lce.add(e);
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Collections.reverse(lce);
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alignmentCigar = new Cigar(lce);
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}
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/** Allows for separate gap opening end extension penalties, no direct backtracking.
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*
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* @param a
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* @param b
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*/
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public void align2(String a, String b) {
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int n = a.length();
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int m = b.length();
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double [][] sw = new double[n+1][m+1];
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// build smith-waterman matrix:
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for ( int i = 1 ; i < n+1 ; i++ ) {
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char a_base = Character.toUpperCase(a.charAt(i-1)); // letter in a at the current pos
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for ( int j = 1 ; j < m+1 ; j++ ) {
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char b_base = Character.toUpperCase(b.charAt(j-1)); // letter in b at the current pos
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double step_diag = sw[i-1][j-1] + wd(a_base,b_base);
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double step_down = 0.0 ;
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for ( int k = 1 ; k < i ; k++ ) step_down = Math.max(step_down,sw[i-k][j]+wk(a_base,'-',k));
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double step_right = 0;
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for ( int k = 1 ; k < j ; k++ ) step_right = Math.max(step_right,sw[i][j-k]+wk('-',b_base,k));
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sw[i][j] = Math.max(0, Math.max(step_diag,Math.max(step_down,step_right)));
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}
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}
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// print(sw,a,b);
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PrimitivePair.Int p = new PrimitivePair.Int();
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double maxscore = 0.0;
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int segment_length = 0; // length of the segment (continuous matches, insertions or deletions)
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// look for largest score. we use >= combined with the traversal direction
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// to ensure that if two scores are equal, the one closer to diagonal gets picked
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for ( int i = 1 ; i < n+1 ; i++ ) {
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if ( sw[i][m] >= maxscore ) { p.first = i; p.second = m ; maxscore = sw[i][m]; }
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}
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for ( int j = 1 ; j < m+1 ; j++ ) {
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if ( sw[n][j] > maxscore ||
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sw[n][j] == maxscore && Math.abs(n-j) < Math.abs(p.first-p.second)) {
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p.first = n;
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p.second = j ;
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maxscore = sw[n][j];
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segment_length = m - j; // end of sequence 2 is overhanging; we will just record it as 'M' segment
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}
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}
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// System.out.println("\ni="+p.first+"; j="+p.second);
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// p holds the position we start backtracking from; we will be assembling a cigar in the backwards order
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// we will be placing all insertions and deletions into sequence b, so the state are named w/regard
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// to that sequence
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int state = MSTATE;
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double [] scores = new double[3];
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List<CigarElement> lce = new ArrayList<CigarElement>(5);
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do {
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// moving left: same base on a, prev base on b = insertion on b:
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scores[ISTATE] = sw[p.first][p.second-1] ;
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scores[DSTATE] = sw[p.first - 1][p.second];
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scores[MSTATE] = sw[p.first-1][p.second-1]; // moving diagonal : match/mismatch
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// System.out.println("i = " + p.first + " ; j = " + p.second);
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// System.out.println("s(M)="+scores[MSTATE]+"; s(D)="+scores[DSTATE]+"; s(I)=" + scores[ISTATE]);
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int new_state = findMaxInd(scores,MSTATE);
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// move to next best location in the sw matrix:
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switch( new_state ) {
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case MSTATE: p.first--; p.second--; break;
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case ISTATE: p.second--; break;
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case DSTATE: p.first--; break;
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}
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// now let's see if the state actually changed:
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if ( new_state == state ) segment_length++;
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else {
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// state changed, lets emit previous segment, whatever it was (Insertion Deletion, or (Mis)Match).
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CigarOperator o=null;
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switch(state) {
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case MSTATE: o = CigarOperator.M; break;
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case ISTATE: o = CigarOperator.I; break;
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case DSTATE: o = CigarOperator.D; break;
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}
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CigarElement e = new CigarElement(segment_length,o);
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lce.add(e);
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segment_length = 1;
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state = new_state;
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}
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} while ( scores[state] != 0 );
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// post-process the last segment we are still keeping
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CigarOperator o=null;
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switch(state) {
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case MSTATE: o = CigarOperator.M; break;
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case ISTATE: o = CigarOperator.I; break;
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case DSTATE: o = CigarOperator.D; break;
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}
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alignment_offset = p.first - p.second;
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segment_length+=p.second;
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CigarElement e = new CigarElement(segment_length,o);
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lce.add(e);
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Collections.reverse(lce);
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alignmentCigar = new Cigar(lce);
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}
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/** Allows for separate gap opening and extension penalties, with backtracking.
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*
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* @param a
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* @param b
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*/
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public void align3(String a, String b) {
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int n = a.length();
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int m = b.length();
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double [][] sw = new double[n+1][m+1];
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int [][] btrack = new int[n+1][m+1];
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// build smith-waterman matrix and keep backtrack info:
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for ( int i = 1 ; i < n+1 ; i++ ) {
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char a_base = Character.toUpperCase(a.charAt(i-1)); // letter in a at the current pos
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for ( int j = 1 ; j < m+1 ; j++ ) {
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char b_base = Character.toUpperCase(b.charAt(j-1)); // letter in b at the current pos
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double step_diag = sw[i-1][j-1] + wd(a_base,b_base);
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double step_down = 0.0 ;
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int kd = 0;
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for ( int k = 1 ; k < i ; k++ ) {
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if ( step_down < sw[i-k][j]+wk(a_base,'-',k) ) {
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step_down=sw[i-k][j]+wk(a_base,'-',k);
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kd = k;
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}
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}
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double step_right = 0;
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int ki = 0;
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for ( int k = 1 ; k < j ; k++ ) {
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if ( step_right < sw[i][j-k]+wk('-',b_base,k) ) {
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step_right=sw[i][j-k]+wk('-',b_base,k);
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ki = k;
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}
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}
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if ( step_down > step_right ) {
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if ( step_down > step_diag ) {
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sw[i][j] = Math.max(0,step_down);
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btrack[i][j] = kd; // positive=vertical
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}
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else {
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sw[i][j] = Math.max(0,step_diag);
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btrack[i][j] = 0; // 0 = diagonal
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}
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} else {
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// step_down < step_right
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if ( step_right > step_diag ) {
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sw[i][j] = Math.max(0,step_right);
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btrack[i][j] = -ki; // negative = horizontal
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} else {
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sw[i][j] = Math.max(0,step_diag);
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btrack[i][j] = 0; // 0 = diagonal
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}
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}
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sw[i][j] = Math.max(0, Math.max(step_diag,Math.max(step_down,step_right)));
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}
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}
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// print(sw,a,b);
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|
PrimitivePair.Int p = new PrimitivePair.Int();
|
||
|
|
double maxscore = 0.0;
|
||
|
|
int segment_length = 0; // length of the segment (continuous matches, insertions or deletions)
|
||
|
|
|
||
|
|
// look for largest score. we use >= combined with the traversal direction
|
||
|
|
// to ensure that if two scores are equal, the one closer to diagonal gets picked
|
||
|
|
for ( int i = 1 ; i < n+1 ; i++ ) {
|
||
|
|
if ( sw[i][m] >= maxscore ) { p.first = i; p.second = m ; maxscore = sw[i][m]; }
|
||
|
|
}
|
||
|
|
for ( int j = 1 ; j < m+1 ; j++ ) {
|
||
|
|
if ( sw[n][j] > maxscore ||
|
||
|
|
sw[n][j] == maxscore && Math.abs(n-j) < Math.abs(p.first-p.second)) {
|
||
|
|
p.first = n;
|
||
|
|
p.second = j ;
|
||
|
|
maxscore = sw[n][j];
|
||
|
|
segment_length = m - j ; // end of sequence 2 is overhanging; we will just record it as 'M' segment
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
System.out.println("\ni="+p.first+"; j="+p.second);
|
||
|
|
|
||
|
|
// p holds the position we start backtracking from; we will be assembling a cigar in the backwards order
|
||
|
|
|
||
|
|
|
||
|
|
// we will be placing all insertions and deletions into sequence b, so the state are named w/regard
|
||
|
|
// to that sequence
|
||
|
|
|
||
|
|
int state = MSTATE;
|
||
|
|
|
||
|
|
double [] scores = new double[3];
|
||
|
|
|
||
|
|
List<CigarElement> lce = new ArrayList<CigarElement>(5);
|
||
|
|
|
||
|
|
do {
|
||
|
|
|
||
|
|
int btr = btrack[p.first][p.second];
|
||
|
|
int step_left = ( btr < 0 ? -btr : 1);
|
||
|
|
int step_up = ( btr > 0 ? btr : 1 );
|
||
|
|
|
||
|
|
// moving left: same base on a, prev base on b = insertion on b:
|
||
|
|
scores[ISTATE] = sw[p.first][p.second-step_left] ;
|
||
|
|
scores[DSTATE] = sw[p.first - step_up][p.second];
|
||
|
|
scores[MSTATE] = sw[p.first-1][p.second-1]; // moving diagonal : match/mismatch
|
||
|
|
|
||
|
|
// System.out.println("i = " + p.first + " ; j = " + p.second);
|
||
|
|
// System.out.println("s(M)="+scores[MSTATE]+"; s(D)="+scores[DSTATE]+"; s(I)=" + scores[ISTATE]);
|
||
|
|
int new_state = findMaxInd(scores,MSTATE);
|
||
|
|
|
||
|
|
int step_length = 1;
|
||
|
|
|
||
|
|
// move to next best location in the sw matrix:
|
||
|
|
switch( new_state ) {
|
||
|
|
case MSTATE: p.first--; p.second--; break;
|
||
|
|
case ISTATE: p.second-=step_left; step_length = step_left; break;
|
||
|
|
case DSTATE: p.first-=step_up; step_length = step_up; break;
|
||
|
|
}
|
||
|
|
|
||
|
|
// now let's see if the state actually changed:
|
||
|
|
if ( new_state == state ) segment_length+=step_length;
|
||
|
|
else {
|
||
|
|
// state changed, lets emit previous segment, whatever it was (Insertion Deletion, or (Mis)Match).
|
||
|
|
CigarOperator o=null;
|
||
|
|
switch(state) {
|
||
|
|
case MSTATE: o = CigarOperator.M; break;
|
||
|
|
case ISTATE: o = CigarOperator.I; break;
|
||
|
|
case DSTATE: o = CigarOperator.D; break;
|
||
|
|
}
|
||
|
|
CigarElement e = new CigarElement(segment_length,o);
|
||
|
|
lce.add(e);
|
||
|
|
segment_length = step_length;
|
||
|
|
state = new_state;
|
||
|
|
}
|
||
|
|
} while ( scores[state] != 0 );
|
||
|
|
|
||
|
|
// post-process the last segment we are still keeping
|
||
|
|
CigarOperator o=null;
|
||
|
|
switch(state) {
|
||
|
|
case MSTATE: o = CigarOperator.M; break;
|
||
|
|
case ISTATE: o = CigarOperator.I; break;
|
||
|
|
case DSTATE: o = CigarOperator.D; break;
|
||
|
|
}
|
||
|
|
alignment_offset = p.first - p.second;
|
||
|
|
segment_length+=p.second;
|
||
|
|
CigarElement e = new CigarElement(segment_length,o);
|
||
|
|
lce.add(e);
|
||
|
|
Collections.reverse(lce);
|
||
|
|
alignmentCigar = new Cigar(lce);
|
||
|
|
}
|
||
|
|
|
||
|
|
public void align4(String a, String b) {
|
||
|
|
int n = a.length();
|
||
|
|
int m = b.length();
|
||
|
|
double [][] sw = new double[n+1][m+1];
|
||
|
|
|
||
|
|
int [][] btrack = new int[n+1][m+1];
|
||
|
|
|
||
|
|
// build smith-waterman matrix and keep backtrack info:
|
||
|
|
for ( int i = 1 ; i < n+1 ; i++ ) {
|
||
|
|
char a_base = Character.toUpperCase(a.charAt(i-1)); // letter in a at the current pos
|
||
|
|
for ( int j = 1 ; j < m+1 ; j++ ) {
|
||
|
|
char b_base = Character.toUpperCase(b.charAt(j-1)); // letter in b at the current pos
|
||
|
|
double step_diag = sw[i-1][j-1] + wd(a_base,b_base);
|
||
|
|
double step_down = 0.0 ;
|
||
|
|
int kd = 0;
|
||
|
|
for ( int k = 1 ; k < i ; k++ ) {
|
||
|
|
if ( step_down < sw[i-k][j]+wk(a_base,'-',k) ) {
|
||
|
|
step_down=sw[i-k][j]+wk(a_base,'-',k);
|
||
|
|
kd = k;
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
double step_right = 0;
|
||
|
|
int ki = 0;
|
||
|
|
for ( int k = 1 ; k < j ; k++ ) {
|
||
|
|
if ( step_right < sw[i][j-k]+wk('-',b_base,k) ) {
|
||
|
|
step_right=sw[i][j-k]+wk('-',b_base,k);
|
||
|
|
ki = k;
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
if ( step_down > step_right ) {
|
||
|
|
if ( step_down > step_diag ) {
|
||
|
|
sw[i][j] = Math.max(0,step_down);
|
||
|
|
btrack[i][j] = kd; // positive=vertical
|
||
|
|
}
|
||
|
|
else {
|
||
|
|
sw[i][j] = Math.max(0,step_diag);
|
||
|
|
btrack[i][j] = 0; // 0 = diagonal
|
||
|
|
}
|
||
|
|
} else {
|
||
|
|
// step_down < step_right
|
||
|
|
if ( step_right > step_diag ) {
|
||
|
|
sw[i][j] = Math.max(0,step_right);
|
||
|
|
btrack[i][j] = -ki; // negative = horizontal
|
||
|
|
} else {
|
||
|
|
sw[i][j] = Math.max(0,step_diag);
|
||
|
|
btrack[i][j] = 0; // 0 = diagonal
|
||
|
|
}
|
||
|
|
}
|
||
|
|
sw[i][j] = Math.max(0, Math.max(step_diag,Math.max(step_down,step_right)));
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
// print(sw,a,b);
|
||
|
|
|
||
|
|
PrimitivePair.Int p = new PrimitivePair.Int();
|
||
|
|
double maxscore = 0.0;
|
||
|
|
int segment_length = 0; // length of the segment (continuous matches, insertions or deletions)
|
||
|
|
|
||
|
|
// look for largest score. we use >= combined with the traversal direction
|
||
|
|
// to ensure that if two scores are equal, the one closer to diagonal gets picked
|
||
|
|
for ( int i = 1 ; i < n+1 ; i++ ) {
|
||
|
|
if ( sw[i][m] >= maxscore ) { p.first = i; p.second = m ; maxscore = sw[i][m]; }
|
||
|
|
}
|
||
|
|
for ( int j = 1 ; j < m+1 ; j++ ) {
|
||
|
|
if ( sw[n][j] > maxscore ||
|
||
|
|
sw[n][j] == maxscore && Math.abs(n-j) < Math.abs(p.first-p.second)) {
|
||
|
|
p.first = n;
|
||
|
|
p.second = j ;
|
||
|
|
maxscore = sw[n][j];
|
||
|
|
segment_length = m - j ; // end of sequence 2 is overhanging; we will just record it as 'M' segment
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
// System.out.println("\ni="+p.first+"; j="+p.second);
|
||
|
|
|
||
|
|
// p holds the position we start backtracking from; we will be assembling a cigar in the backwards order
|
||
|
|
|
||
|
|
|
||
|
|
// we will be placing all insertions and deletions into sequence b, so the state are named w/regard
|
||
|
|
// to that sequence
|
||
|
|
|
||
|
|
int state = MSTATE;
|
||
|
|
|
||
|
|
double [] scores = new double[3];
|
||
|
|
|
||
|
|
List<CigarElement> lce = new ArrayList<CigarElement>(5);
|
||
|
|
|
||
|
|
do {
|
||
|
|
|
||
|
|
int btr = btrack[p.first][p.second];
|
||
|
|
int step_left = ( btr < 0 ? -btr : 1);
|
||
|
|
int step_up = ( btr > 0 ? btr : 1 );
|
||
|
|
|
||
|
|
int new_state = -1;
|
||
|
|
if ( btr > 0 ) new_state = DSTATE;
|
||
|
|
else if ( btr < 0 ) new_state = ISTATE;
|
||
|
|
else new_state = MSTATE;
|
||
|
|
|
||
|
|
int step_length = 1;
|
||
|
|
|
||
|
|
// move to next best location in the sw matrix:
|
||
|
|
switch( new_state ) {
|
||
|
|
case MSTATE: p.first--; p.second--; break;
|
||
|
|
case ISTATE: p.second-=step_left; step_length = step_left; break;
|
||
|
|
case DSTATE: p.first-=step_up; step_length = step_up; break;
|
||
|
|
}
|
||
|
|
|
||
|
|
// now let's see if the state actually changed:
|
||
|
|
if ( new_state == state ) segment_length+=step_length;
|
||
|
|
else {
|
||
|
|
// state changed, lets emit previous segment, whatever it was (Insertion Deletion, or (Mis)Match).
|
||
|
|
CigarOperator o=null;
|
||
|
|
switch(state) {
|
||
|
|
case MSTATE: o = CigarOperator.M; break;
|
||
|
|
case ISTATE: o = CigarOperator.I; break;
|
||
|
|
case DSTATE: o = CigarOperator.D; break;
|
||
|
|
}
|
||
|
|
CigarElement e = new CigarElement(segment_length,o);
|
||
|
|
lce.add(e);
|
||
|
|
segment_length = step_length;
|
||
|
|
state = new_state;
|
||
|
|
}
|
||
|
|
} while ( sw[p.first][p.second] != 0 );
|
||
|
|
|
||
|
|
// post-process the last segment we are still keeping
|
||
|
|
CigarOperator o=null;
|
||
|
|
switch(state) {
|
||
|
|
case MSTATE: o = CigarOperator.M; break;
|
||
|
|
case ISTATE: o = CigarOperator.I; break;
|
||
|
|
case DSTATE: o = CigarOperator.D; break;
|
||
|
|
}
|
||
|
|
alignment_offset = p.first - p.second;
|
||
|
|
segment_length+=p.second;
|
||
|
|
CigarElement e = new CigarElement(segment_length,o);
|
||
|
|
lce.add(e);
|
||
|
|
Collections.reverse(lce);
|
||
|
|
alignmentCigar = new Cigar(lce);
|
||
|
|
}
|
||
|
|
|
||
|
|
private int w(char x, char y) {
|
||
|
|
if ( x == y ) return 2; // match
|
||
|
|
if ( x == '-' || y == '-' ) return -1; // gap
|
||
|
|
return -1; // mismatch
|
||
|
|
}
|
||
|
|
|
||
|
|
private double wd ( char x, char y ) {
|
||
|
|
if ( x== y ) return w_match;
|
||
|
|
else return w_mismatch;
|
||
|
|
}
|
||
|
|
|
||
|
|
private double wk(char x, char y, int k) {
|
||
|
|
return w_open+(k-1)*w_extend; // gap
|
||
|
|
// return -1.0 ; // no extension penalty
|
||
|
|
// return -1.0-Math.log(k+1); // weak extension penalty
|
||
|
|
}
|
||
|
|
|
||
|
|
/** Returns index of the maximum element in array s. If there is a tie, and one of the tied indices is
|
||
|
|
* pref_id, then it will be preferred and returned.
|
||
|
|
* @param s
|
||
|
|
* @param pref_id
|
||
|
|
* @return
|
||
|
|
*/
|
||
|
|
private int findMaxInd(int[] s, int pref_id) {
|
||
|
|
int imax = 0;
|
||
|
|
int maxval = s[0];
|
||
|
|
for ( int i = 1; i < s.length ; i++ ) {
|
||
|
|
if ( s[i] > maxval || i == pref_id && Math.abs(s[i] - maxval) < 0.0001 ) {
|
||
|
|
imax = i;
|
||
|
|
maxval = s[i];
|
||
|
|
}
|
||
|
|
}
|
||
|
|
return imax;
|
||
|
|
}
|
||
|
|
|
||
|
|
private int findMaxInd(double[] s, int pref_id) {
|
||
|
|
int imax = 0;
|
||
|
|
double maxval = s[0];
|
||
|
|
for ( int i = 1; i < s.length ; i++ ) {
|
||
|
|
if ( s[i] > maxval + 0.0001 || i == pref_id && Math.abs(s[i] - maxval) < 0.0001 ) {
|
||
|
|
imax = i;
|
||
|
|
maxval = s[i];
|
||
|
|
}
|
||
|
|
}
|
||
|
|
return imax;
|
||
|
|
}
|
||
|
|
|
||
|
|
private void print(int[][] s) {
|
||
|
|
for ( int i = 0 ; i < s.length ; i++) {
|
||
|
|
for ( int j = 0; j < s[i].length ; j++ ) {
|
||
|
|
System.out.printf(" %4d",s[i][j]);
|
||
|
|
}
|
||
|
|
System.out.println();
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
private void print(double[][] s) {
|
||
|
|
for ( int i = 0 ; i < s.length ; i++) {
|
||
|
|
for ( int j = 0; j < s[i].length ; j++ ) {
|
||
|
|
System.out.printf(" %4g",s[i][j]);
|
||
|
|
}
|
||
|
|
System.out.println();
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
private void print(int[][] s, String a, String b) {
|
||
|
|
|
||
|
|
System.out.print(" ");
|
||
|
|
for ( int j = 1 ; j < s[0].length ; j++) System.out.printf(" %4c",b.charAt(j-1)) ;
|
||
|
|
System.out.println();
|
||
|
|
|
||
|
|
for ( int i = 0 ; i < s.length ; i++) {
|
||
|
|
if ( i > 0 ) System.out.print(a.charAt(i-1));
|
||
|
|
else System.out.print(' ');
|
||
|
|
System.out.print(" ");
|
||
|
|
for ( int j = 0; j < s[i].length ; j++ ) {
|
||
|
|
System.out.printf(" %4d",s[i][j]);
|
||
|
|
}
|
||
|
|
System.out.println();
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
|
||
|
|
private void print(double[][] s, String a, String b) {
|
||
|
|
|
||
|
|
System.out.print("");
|
||
|
|
for ( int j = 1 ; j < s[0].length ; j++) System.out.printf(" %4c",b.charAt(j-1)) ;
|
||
|
|
System.out.println();
|
||
|
|
|
||
|
|
for ( int i = 0 ; i < s.length ; i++) {
|
||
|
|
if ( i > 0 ) System.out.print(a.charAt(i-1));
|
||
|
|
else System.out.print(' ');
|
||
|
|
System.out.print(" ");
|
||
|
|
for ( int j = 0; j < s[i].length ; j++ ) {
|
||
|
|
System.out.printf(" %2.1f",s[i][j]);
|
||
|
|
}
|
||
|
|
System.out.println();
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
public String toString() {
|
||
|
|
StringBuilder bmm = new StringBuilder();
|
||
|
|
StringBuilder b1 = new StringBuilder();
|
||
|
|
StringBuilder b2 = new StringBuilder();
|
||
|
|
|
||
|
|
int pos1 = 0;
|
||
|
|
int pos2 = 0;
|
||
|
|
if ( alignment_offset < 0 ) {
|
||
|
|
for ( ; pos2 < -alignment_offset ; pos2++ ) {
|
||
|
|
b1.append(' ');
|
||
|
|
b2.append(s2.charAt(pos2));
|
||
|
|
bmm.append(' ');
|
||
|
|
}
|
||
|
|
// now pos2 = -alignment_offset;
|
||
|
|
} else {
|
||
|
|
for ( ; pos1 < alignment_offset ; pos1++ ) {
|
||
|
|
b2.append(' ');
|
||
|
|
b1.append(s1.charAt(pos1));
|
||
|
|
bmm.append(' ');
|
||
|
|
}
|
||
|
|
// now pos1 = alignment_offset
|
||
|
|
}
|
||
|
|
/* debug prints: */
|
||
|
|
// System.out.println(AlignmentUtils.toString(getCigar()));
|
||
|
|
// System.out.println("seq1l="+s1.length()+"; seq2l=" + s2.length());
|
||
|
|
// System.out.println("offset="+alignment_offset);
|
||
|
|
// System.out.println("pos1="+pos1+"; pos2=" + pos2);
|
||
|
|
/**/
|
||
|
|
for ( int i = 0 ; i < getCigar().numCigarElements() ; i++ ) {
|
||
|
|
CigarElement ce = getCigar().getCigarElement(i) ;
|
||
|
|
switch( ce.getOperator() ) {
|
||
|
|
case M:
|
||
|
|
int z = ( i == 0 ? pos2 : 0); // if we are in the first element and seq overhangs to the left,
|
||
|
|
// start inside the first segment, at the position where actual matches begin
|
||
|
|
// check separately for pos1 < s1.length() since seq2 is allowed to overhang beyond seq1's end
|
||
|
|
for ( ; z < ce.getLength() && pos1 < s1.length() ; z++ ) {
|
||
|
|
// System.out.println("pos1="+pos1+"; pos2="+pos2+"; k="+z);
|
||
|
|
if ( Character.toUpperCase(s1.charAt(pos1)) !=
|
||
|
|
Character.toUpperCase(s2.charAt(pos2)) ) bmm.append('*');
|
||
|
|
else bmm.append(' ');
|
||
|
|
b1.append(s1.charAt(pos1++));
|
||
|
|
b2.append(s2.charAt(pos2++));
|
||
|
|
}
|
||
|
|
break;
|
||
|
|
case I:
|
||
|
|
for ( int k = 0 ; k < ce.getLength() ; k++ ) {
|
||
|
|
b1.append('+');
|
||
|
|
bmm.append('+');
|
||
|
|
b2.append(s2.charAt(pos2++));
|
||
|
|
}
|
||
|
|
break;
|
||
|
|
case D:
|
||
|
|
for ( int k = 0 ; k < ce.getLength() ; k++ ) {
|
||
|
|
b1.append(s1.charAt(pos1++));
|
||
|
|
bmm.append('-');
|
||
|
|
b2.append('-');
|
||
|
|
}
|
||
|
|
break;
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
bmm.append('\n');
|
||
|
|
b1.append(s1,pos1,s1.length());
|
||
|
|
bmm.append(b1);
|
||
|
|
bmm.append('\n');
|
||
|
|
b2.append(s2,pos2,s2.length());
|
||
|
|
bmm.append(b2);
|
||
|
|
bmm.append('\n');
|
||
|
|
|
||
|
|
return bmm.toString();
|
||
|
|
}
|
||
|
|
|
||
|
|
public static void testMe() {
|
||
|
|
/* String s1 = "ACCTGGTGTATATAGGGTAAGGCTGAT";
|
||
|
|
String s2 = "TGTATATAGGGTAAGG";
|
||
|
|
|
||
|
|
testMe(s1,s2);
|
||
|
|
|
||
|
|
s1 = "GGTAAGGC";
|
||
|
|
s2 = "GGTCTCAA";
|
||
|
|
|
||
|
|
testMe(s1,s2);
|
||
|
|
|
||
|
|
s1 = "ACCTGGTGTATATAGGGTAAGGCTGAT";
|
||
|
|
s2 = "TGTTAGGGTCTCAAGG";
|
||
|
|
testMe(s1,s2);
|
||
|
|
|
||
|
|
|
||
|
|
s1 = "ACCTGGTGTATATAGGGTAAGGCTGAT";
|
||
|
|
s2 = "TAGGGTAAGGCTGATCCATGTACCG" ;
|
||
|
|
testMe(s1,s2);
|
||
|
|
|
||
|
|
s1 = "ACCTGGTGTATATAGGGTAAGGCTGAT";
|
||
|
|
s2 = "CCGTATCATTACCTGGTGTATATAGG";
|
||
|
|
testMe(s1,s2);
|
||
|
|
|
||
|
|
s1 = "GGTGTATATAGGGT" ;
|
||
|
|
s2 = "TGTTAGGG";
|
||
|
|
testMe(s1,s2);
|
||
|
|
|
||
|
|
s1 = "AGACAGAGAGAAGG";
|
||
|
|
s2 = "AGACAGAGAAGG";
|
||
|
|
testMe(s1,s2);
|
||
|
|
*/
|
||
|
|
// String s1 = "CCAGCACACAGGTATCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTTTTTTGA";
|
||
|
|
// String s2 = "CCAGCACACATCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTTTTTTGA";
|
||
|
|
|
||
|
|
// String s1 = "CCCATCTGTCTCCAATCTGCTGTTTTCCAAAAATTAGGGAACTTCAGTTTTCCCTTTGATACTCTGTATTTCTACCAACCACAACGCCAGGGCTGTCCTGCTTCTACAAGTGACAATGACAAATATAGGCCTGAAGGAAGATG";
|
||
|
|
// String s2 = "AAAATCTGTTTCCAATCTACTGTTTTCCAAAAATTAGGGAAGTTCAGTTTTCCCTTTGATACTCTGTTTCTACCAATCC";
|
||
|
|
String s1 = "CCCATCTGTCTCCAATCTGCTGTTTTCCAAAAATTAGGGAACTTCAGTTTTCCCTTTGATACTCTGTATTTCTACCAACCACAACGCCAGGGCTGTCCTGCTTCTACAAGTGACAATGACAAATATAGGCCTGAAGGAAGATG";
|
||
|
|
String s2 = "AAAATCTGTCTCCAATCTACTGTTTTCCAAAAATTAGGGAAGTTCAGTTTTCCCTTTGATACTCTGTTTCTACCAATCC";
|
||
|
|
testMe(s1,s2);
|
||
|
|
}
|
||
|
|
|
||
|
|
public static void testMe(String s1, String s2) {
|
||
|
|
|
||
|
|
SWPairwiseAlignment swpa = new SWPairwiseAlignment(s1,s2,3.0,-1.0,-4,-0.5);
|
||
|
|
|
||
|
|
System.out.println(AlignmentUtils.toString(swpa.getCigar()));
|
||
|
|
// SequencePile sp = new SequencePile(s1);
|
||
|
|
// sp.addAlignedSequence(s2,false,swpa.getCigar(),swpa.getAlignmentStart2wrt1());
|
||
|
|
// System.out.println();
|
||
|
|
// System.out.println(sp.format());
|
||
|
|
|
||
|
|
System.out.println("--------\n"+swpa.toString());
|
||
|
|
|
||
|
|
//sp.colorprint(false);
|
||
|
|
}
|
||
|
|
|
||
|
|
public static void main(String argv[]) {
|
||
|
|
if ( argv.length > 0 ) testMe(argv[0],argv[1]);
|
||
|
|
else testMe();
|
||
|
|
}
|
||
|
|
}
|