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fixed bug in calculation of alignment start offset for negative offsets; toString() added 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@170 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-03-24 18:05:28 +00:00
parent 9aa1ccd9b7
commit 8ea8a74fbf
1 changed files with 64 additions and 5 deletions
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69
java/src/org/broadinstitute/sting/playground/indels/SWPairwiseAlignment.java
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@ -147,7 +147,7 @@ public class SWPairwiseAlignment {
lce.add(e);
Collections.reverse(lce);
alignmentCigar = new Cigar(lce);
alignment_offset = p.first;
alignment_offset = p.first - p.second;
}
/** Allows for separate gap opening end extension penalties, no direct backtracking.
@ -254,7 +254,7 @@ public class SWPairwiseAlignment {
lce.add(e);
Collections.reverse(lce);
alignmentCigar = new Cigar(lce);
alignment_offset = p.first;
alignment_offset = p.first - p.second ;
}
@ -402,7 +402,7 @@ public void align3(String a, String b) {
lce.add(e);
Collections.reverse(lce);
alignmentCigar = new Cigar(lce);
alignment_offset = p.first;
alignment_offset = p.first - p.second;
}
@ -506,6 +506,57 @@ public void align3(String a, String b) {
}
}
public String toString() {
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));
}
// now pos2 = -alignment_offset;
} else {
for ( ; pos1 < alignment_offset ; pos1++ ) {
b2.append(' ');
b1.append(s1.charAt(pos1));
}
// now pos1 = alignment_offset
}
for ( int i = 0 ; i < getCigar().numCigarElements() ; i++ ) {
CigarElement ce = getCigar().getCigarElement(i) ;
switch( ce.getOperator() ) {
case M:
int z = ce.getLength();
b1.append(s1, pos1, pos1+z);
b2.append(s2, pos2, pos2+z);
pos1+=z; pos2+=z;
break;
case I:
for ( int k = 0 ; k < ce.getLength() ; k++ ) {
b1.append('+');
b2.append(s2.charAt(pos2++));
}
break;
case D:
for ( int k = 0 ; k < ce.getLength() ; k++ ) {
b1.append(s1.charAt(pos1++));
b2.append('-');
}
break;
}
}
b1.append(s1,pos1,s1.length());
b2.append(s2,pos2,s2.length());
b1.append('\n');
b1.append(b2);
b1.append('\n');
return b1.toString();
}
public static void testMe() {
// String s1 = "ACCTGGTGTATATAGGGTAAGGCTGAT";
// String s2 = "TGTATATAGGGTAAGG";
@ -513,8 +564,14 @@ public void align3(String a, String b) {
// String s1 = "GGTAAGGC";
// String s2 = "GGTCTCAA";
String s1 = "ACCTGGTGTATATAGGGTAAGGCTGAT";
String s2 = "TGTTAGGGTCTCAAGG";
// String s1 = "ACCTGGTGTATATAGGGTAAGGCTGAT";
// String s2 = "TGTTAGGGTCTCAAGG";
// String s1 = "ACCTGGTGTATATAGGGTAAGGCTGAT";
// String s2 = "TAGGGTAAGGCTGATCCATGTACCG" ;
String s1 = "ACCTGGTGTATATAGGGTAAGGCTGAT";
String s2 = "CCGTATCATTACCTGGTGTATATAGG";
// String s1 = "GGTGTATATAGGGT" ;
// String s2 = "TGTTAGGG";
@ -541,6 +598,8 @@ public void align3(String a, String b) {
System.out.println();
System.out.println(sp.format());
System.out.println("--------\n"+swpa.toString());
//sp.colorprint(false);
}