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some reformatting and logic cleanup in the comparison functions 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@132 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-03-22 15:36:56 +00:00
parent dfe50ce773
commit f7ad17016d
1 changed files with 24 additions and 8 deletions
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32
core/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
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@ -186,35 +186,51 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
// //
// Comparison operations // Comparison operations
// //
public static int compareContigs( final String thisContig, final String thatContig ) { public static int compareContigs( final String thisContig, final String thatContig )
{
if ( thisContig == thatContig ) if ( thisContig == thatContig )
{
assert(false);
return 0; return 0;
}
if ( refContigOrdering != null ) { assert refContigOrdering.containsKey(thisContig);// : this;
if ( ! refContigOrdering.containsKey(thisContig) ) { assert refContigOrdering.containsKey(thatContig);// : that;
if ( ! refContigOrdering.containsKey(thatContig) ) {
if ( refContigOrdering != null )
{
if ( ! refContigOrdering.containsKey(thisContig) )
{
if ( ! refContigOrdering.containsKey(thatContig) )
{
// Use regular sorted order // Use regular sorted order
return thisContig.compareTo(thatContig); return thisContig.compareTo(thatContig);
} }
else { else
{
// this is always bigger if that is in the key set // this is always bigger if that is in the key set
return 1; return 1;
} }
} }
else if ( ! refContigOrdering.containsKey(thatContig) ) else if ( ! refContigOrdering.containsKey(thatContig) )
{
return -1; return -1;
else { }
else
{
assert refContigOrdering.containsKey(thisContig);// : this; assert refContigOrdering.containsKey(thisContig);// : this;
assert refContigOrdering.containsKey(thatContig);// : that; assert refContigOrdering.containsKey(thatContig);// : that;
final int thisO = refContigOrdering.get(thisContig); final int thisO = refContigOrdering.get(thisContig);
final int thatO = refContigOrdering.get(thatContig); final int thatO = refContigOrdering.get(thatContig);
if ( thisO < thatO ) return -1; if ( thisO < thatO ) return -1;
if ( thisO > thatO ) return 1; if ( thisO > thatO ) return 1;
return 0; return 0;
} }
} }
else { else
{
return thisContig.compareTo(thatContig); return thisContig.compareTo(thatContig);
} }
} }
@ -235,4 +251,4 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
if ( this.getStop() > that.getStop() ) return 1; if ( this.getStop() > that.getStop() ) return 1;
return 0; return 0;
} }
} }