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Print on multiple rows in standalone command line mode when the sequences are too long 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5779 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2011-05-09 13:51:00 +00:00
parent bf40351094
commit 0861451726
1 changed files with 32 additions and 3 deletions
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35
java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java
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@ -432,6 +432,10 @@ public class SWPairwiseAlignment {
}
static void printAlignment(SWPairwiseAlignment a, byte[] ref, byte[] read) {
printAlignment(a,ref,read,100);
}
static void printAlignment(SWPairwiseAlignment a, byte[] ref, byte[] read, int width) {
StringBuilder bread = new StringBuilder();
StringBuilder bref = new StringBuilder();
StringBuilder match = new StringBuilder();
@ -443,6 +447,7 @@ public class SWPairwiseAlignment {
Cigar cigar = a.getCigar();
if ( offset < 0 ) {
for ( ; j < (-offset) ; j++ ) {
bread.append((char)read[j]);
@ -498,9 +503,33 @@ public class SWPairwiseAlignment {
for ( ; i < ref.length; i++ ) bref.append((char)ref[i]);
for ( ; j < read.length; j++ ) bread.append((char)read[j]);
System.out.println(match);
System.out.println(bread);
System.out.println(bref);
int pos = 0 ;
int maxlength = Math.max(match.length(),Math.max(bread.length(),bref.length()));
while ( pos < maxlength ) {
print_cautiously(match,pos,width);
print_cautiously(bread,pos,width);
print_cautiously(bref,pos,width);
System.out.println();
pos += width;
}
}
/** String builder's substring is extremely stupid: instead of trimming and/or returning an empty
* string when one end/both ends of the interval are out of range, it crashes with an
* exception. This utility function simply prints the substring if the interval is within the index range
* or trims accordingly if it is not.
* @param s
* @param start
* @param width
*/
private static void print_cautiously(StringBuilder s, int start, int width) {
if ( start >= s.length() ) {
System.out.println();
return;
}
int end = Math.min(start+width,s.length());
System.out.println(s.substring(start,end));
}
// BELOW: main() method for testing; old implementations of the core methods are commented out below;