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Failed to include some required GenomeLoc utilities in my last commit. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5397 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2011-03-07 23:00:17 +00:00
parent 02006954bc
commit 85ff983a59
1 changed files with 21 additions and 0 deletions
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21
java/src/org/broadinstitute/sting/utils/GenomeLoc.java
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@ -122,6 +122,17 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable, Serializable
Math.max( getStop(), that.getStop()) ); Math.max( getStop(), that.getStop()) );
} }
/**
* Splits the contig into to regions: [start,split point) and [split point, end].
* @param splitPoint The point at which to split the contig. Must be contained in the given interval.
* @return A two element array consisting of the genome loc before the split and the one after.
*/
public GenomeLoc[] split(final int splitPoint) {
if(splitPoint < getStart() || splitPoint > getStop())
throw new ReviewedStingException(String.format("Unable to split contig %s at split point %d; split point is not contained in region.",this,splitPoint));
return new GenomeLoc[] { new GenomeLoc(getContig(),contigIndex,getStart(),splitPoint-1), new GenomeLoc(getContig(),contigIndex,splitPoint,getStop()) };
}
public GenomeLoc intersect( GenomeLoc that ) throws ReviewedStingException { public GenomeLoc intersect( GenomeLoc that ) throws ReviewedStingException {
if(GenomeLoc.isUnmapped(this) || GenomeLoc.isUnmapped(that)) { if(GenomeLoc.isUnmapped(this) || GenomeLoc.isUnmapped(that)) {
if(! GenomeLoc.isUnmapped(this) || !GenomeLoc.isUnmapped(that)) if(! GenomeLoc.isUnmapped(this) || !GenomeLoc.isUnmapped(that))
@ -171,6 +182,16 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable, Serializable
return ( comparison == -1 || ( comparison == 0 && this.getStop() < that.getStart() )); return ( comparison == -1 || ( comparison == 0 && this.getStop() < that.getStart() ));
} }
/**
* Tests whether any portion of this contig is before that contig.
* @param that Other contig to test.
* @return True if the start of this contig is before the start of the that contig.
*/
public final boolean startsBefore(final GenomeLoc that) {
int comparison = this.compareContigs(that);
return ( comparison == -1 || ( comparison == 0 && this.getStart() < that.getStart() ));
}
/** /**
* Tests whether this contig is completely after contig 'that'. * Tests whether this contig is completely after contig 'that'.
* @param that Contig to test against. * @param that Contig to test against.