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added List<Transcript> getTranscripts(); also more comments added 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@894 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-06-04 16:25:14 +00:00
parent 67112c79a1
commit bcc7bacba1
1 changed files with 11 additions and 1 deletions
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12
java/src/org/broadinstitute/sting/gatk/refdata/rodRefSeq.java
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@ -52,7 +52,8 @@ public class rodRefSeq extends BasicReferenceOrderedDatum {
/** Returns true if the current position this ROD is associated with is within the coding interval for at least /** Returns true if the current position this ROD is associated with is within the coding interval for at least
* one of the annotated transcripts. NOTE: "coding" interval is defined as a single genomic interval, so it * one of the annotated transcripts. NOTE: "coding" interval is defined as a single genomic interval, so it
* does not include the UTRs of the outermost exons, but it includes introns between exons spliced into a * does not include the UTRs of the outermost exons, but it includes introns between exons spliced into a
* transcript, or internal exons that are not spliced into a given transcript. @see isExon(). * transcript, or internal exons that are not spliced into a given transcript. To check that a position is
* indeed within an exon but not in UTR, use isExon() && isCoding(). @see isExon().
* @return * @return
*/ */
public boolean isCoding() { public boolean isCoding() {
@ -76,6 +77,15 @@ public class rodRefSeq extends BasicReferenceOrderedDatum {
return false; return false;
} }
/** Returns all annotated transcripts overlapping with the current position as an immutable list.
* "Overlap" is defined as position being within genomic interval corresponding to the whole
* transcript start/transcript stop coordinates, thus the position can be still in a UTR, in intron, or
* in an internal exon that is actually not spliced into the specific transcript. Use isExon(), isCoding() of
* this ROD class, or query individual Transcript objects returned by this method to get more details.
* @return
*/
public List<Transcript> getTranscripts() { return Collections.unmodifiableList(records) ; }
@Override @Override
public String repl() { public String repl() {
throw new StingException("repl() is not implemented yet"); throw new StingException("repl() is not implemented yet");