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Cleanup the getLIBS function in LocusIterator 

-- Now throws an UnsupportedOperationException in the base class.  Only LocusView implements this function and actually returns the LIBS
This commit is contained in:
Mark DePristo 2013-01-25 10:13:12 -05:00
parent f7b80116d6
commit 008b617577
2 changed files with 15 additions and 8 deletions
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8
public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java
View File

@ -214,7 +214,13 @@ public abstract class LocusView extends LocusIterator implements View {
return locus.containsP(location);
}
// TODO -- remove me
/**
* {@inheritDoc}
*
* Since this class has an actual LIBS, so this function will never throw an exception
*
* @return the LocusIteratorByState used by this view to get pileups
*/
@Override
public LocusIteratorByState getLIBS() {
return loci.getLIBS();

15
public/java/src/org/broadinstitute/sting/utils/locusiterator/LocusIterator.java
View File

@ -34,11 +34,6 @@ import java.util.Iterator;
* Iterator that traverses a SAM File, accumulating information on a per-locus basis
*/
public abstract class LocusIterator implements Iterable<AlignmentContext>, CloseableIterator<AlignmentContext> {
// -----------------------------------------------------------------------------------------------------------------
//
// constructors and other basic operations
//
// -----------------------------------------------------------------------------------------------------------------
public Iterator<AlignmentContext> iterator() {
return this;
}
@ -50,9 +45,15 @@ public abstract class LocusIterator implements Iterable<AlignmentContext>, Close
public abstract boolean hasNext();
public abstract AlignmentContext next();
// TODO -- remove me when ART testing is done
/**
* Get, if possible, the underlying LocusIteratorByState from this LocusIterator.
*
* @throws UnsupportedOperationException if we don't support this operation
*
* @return a non-null locus iterator by state
*/
public LocusIteratorByState getLIBS() {
return null;
throw new UnsupportedOperationException("This locus iterator does not support getting the underlying LocusIteratorByState");
}
public void remove() {