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getBoundRods() convenience method 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1595 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2009-09-12 19:07:57 +00:00
parent 4e1eded389
commit 58105636c8
1 changed files with 17 additions and 0 deletions
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17
java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
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@ -4,6 +4,7 @@ import org.apache.log4j.Logger;
import java.util.Collection; import java.util.Collection;
import java.util.HashMap; import java.util.HashMap;
import java.util.LinkedList;
/** /**
* This class represents the Reference Metadata available at a particular site in the genome. It can be * This class represents the Reference Metadata available at a particular site in the genome. It can be
@ -85,6 +86,22 @@ public class RefMetaDataTracker {
return map.values(); return map.values();
} }
/**
* Get all of the RODs at the current site
*
* @return
*/
public Collection<ReferenceOrderedDatum> getBoundRods() {
LinkedList<ReferenceOrderedDatum> bound = new LinkedList<ReferenceOrderedDatum>();
for ( ReferenceOrderedDatum value : map.values() ) {
if ( value != null )
bound.add(value);
}
return bound;
}
/** /**
* Binds the reference ordered datum ROD to name at this site. Should be used only but the traversal * Binds the reference ordered datum ROD to name at this site. Should be used only but the traversal
* system to provide access to RODs in a structured way to the walkers. * system to provide access to RODs in a structured way to the walkers.