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Added startsBefore, startsAfter, and minDistance [calculates distance between any pair of bases in the two GenomeLocs] 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4531 348d0f76-0448-11de-a6fe-93d51630548a
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fromer 2010-10-20 19:12:34 +00:00
parent 4f77581087
commit 55230ce5f3
1 changed files with 31 additions and 1 deletions
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32
java/src/org/broadinstitute/sting/utils/GenomeLoc.java
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@ -201,7 +201,7 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable, Serializable
}
public final int minus( final GenomeLoc that ) {
if ( this.contigIndex == that.contigIndex )
if ( this.onSameContig(that) )
return (int) (this.getStart() - that.getStart());
else
return Integer.MAX_VALUE;
@ -225,6 +225,36 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable, Serializable
return ( comparison == 1 || ( comparison == 0 && this.getStart() > that.getStop() ));
}
public final boolean startsBefore( GenomeLoc that ) {
int comparison = this.compareContigs(that);
return ( comparison == -1 || ( comparison == 0 && this.getStart() < that.getStart() ));
}
public final boolean startsAfter( GenomeLoc that ) {
int comparison = this.compareContigs(that);
return ( comparison == 1 || ( comparison == 0 && this.getStart() > that.getStart() ));
}
// Return the minimum distance between any pair of bases in this and that GenomeLocs:
public final int minDistance( final GenomeLoc that ) {
if (!this.onSameContig(that))
return Integer.MAX_VALUE;
int minDistance;
if (this.isBefore(that))
minDistance = distanceFirstStopToSecondStart(this, that);
else if (that.isBefore(this))
minDistance = distanceFirstStopToSecondStart(that, this);
else // this and that overlap [and possibly one contains the other]:
minDistance = 0;
return minDistance;
}
private static int distanceFirstStopToSecondStart(GenomeLoc locFirst, GenomeLoc locSecond) {
return (int) (locSecond.getStart() - locFirst.getStop());
}
/**