53 lines
2.2 KiB
Java
53 lines
2.2 KiB
Java
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package org.broadinstitute.sting.gatk.refdata;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import java.util.List;
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/**
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* Created by IntelliJ IDEA.
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* User: asivache
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* Date: Sep 22, 2009
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* Time: 5:22:30 PM
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* To change this template use File | Settings | File Templates.
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*/
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public interface Transcript {
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/** Returns id of the transcript (RefSeq NM_* id) */
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public String getTranscriptId();
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/** Returns coding strand of the transcript, 1 or -1 for positive or negative strand, respectively */
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public int getStrand();
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/** Returns transcript's full genomic interval (includes all exons with UTRs) */
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public GenomeLoc getLocation();
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/** Returns genomic interval of the coding sequence (does not include
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* UTRs, but still includes introns, since it's a single interval on the DNA)
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*/
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public GenomeLoc getCodingLocation();
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/** Name of the gene this transcript corresponds to (typically NOT gene id such as Entrez etc,
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* but the implementation can decide otherwise)
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*/
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public String getGeneName();
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/** Number of exons in this transcript */
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public int getNumExons();
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/** Genomic location of the n-th exon; expected to throw an exception (runtime) if n is out of bounds */
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public GenomeLoc getExonLocation(int n);
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/** Returns the list of all exons in this transcript, as genomic intervals */
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public List<GenomeLoc> getExons();
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/** Returns true if the specified interval 'that' overlaps with the full genomic interval of this transcript */
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public boolean overlapsP (GenomeLoc that);
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/** Returns true if the specified interval 'that' overlaps with the coding genomic interval of this transcript.
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* NOTE: since "coding interval" is still a single genomic interval, it will not contain UTRs of the outermost exons,
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* but it will still contain introns and/or exons internal to this genomic locus that are not spliced into this transcript.
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* @see #overlapsExonP
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*/
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public boolean overlapsCodingP (GenomeLoc that);
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/** Returns true if the specified interval 'that' overlaps with any of the exons actually spliced into this transcript */
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public boolean overlapsExonP (GenomeLoc that);
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}
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