From 8fa4c93f5a812fec51902fab37dfd4a45a5cf649 Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 23 Sep 2009 18:13:31 +0000
Subject: [PATCH] Transcript is now simply an interface

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1696 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/refdata/Transcript.java        | 52 +++++++++++++++++++
 1 file changed, 52 insertions(+)
 create mode 100644 java/src/org/broadinstitute/sting/gatk/refdata/Transcript.java

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/Transcript.java b/java/src/org/broadinstitute/sting/gatk/refdata/Transcript.java
new file mode 100644
index 000000000..688ffafee
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/Transcript.java
@@ -0,0 +1,52 @@
+package org.broadinstitute.sting.gatk.refdata;
+
+import org.broadinstitute.sting.utils.GenomeLoc;
+
+import java.util.List;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: asivache
+ * Date: Sep 22, 2009
+ * Time: 5:22:30 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public interface Transcript {
+
+    /** Returns id of the transcript (RefSeq NM_* id) */
+    public String getTranscriptId();
+    /** Returns coding strand of the transcript, 1 or -1 for positive or negative strand, respectively */
+    public int getStrand();
+    /** Returns transcript's full genomic interval (includes all exons with UTRs) */
+    public GenomeLoc getLocation();
+    /** Returns genomic interval of the coding sequence (does not include
+     * UTRs, but still includes introns, since it's a single interval on the DNA)
+     */
+    public GenomeLoc getCodingLocation();
+    /** Name of the gene this transcript corresponds to (typically NOT gene id such as Entrez etc,
+     * but the implementation can decide otherwise)
+     */
+    public String getGeneName();
+    /** Number of exons in this transcript */
+    public int getNumExons();
+    /** Genomic location of the n-th exon; expected to throw an exception (runtime) if n is out of bounds */
+    public GenomeLoc getExonLocation(int n);
+
+    /** Returns the list of all exons in this transcript, as genomic intervals */
+    public List<GenomeLoc> getExons();
+
+    /** Returns true if the specified interval 'that' overlaps with the full genomic interval of this transcript */
+    public boolean overlapsP (GenomeLoc that);
+
+    /** Returns true if the specified interval 'that' overlaps with the coding genomic interval of this transcript.
+      * NOTE: since "coding interval" is still a single genomic interval, it will not contain UTRs of the outermost exons,
+      * but it will still contain introns and/or exons internal to this genomic locus that are not spliced into this transcript.
+      * @see #overlapsExonP
+      */
+    public boolean overlapsCodingP (GenomeLoc that);
+
+    /** Returns true if the specified interval 'that' overlaps with any of the exons actually spliced into this transcript */
+    public boolean overlapsExonP (GenomeLoc that);
+
+
+}