From 4660937a02602e6986e7c0753699b22afa26347e Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 4 Oct 2016 13:50:02 +0100
Subject: [PATCH] JAL-2232 added test that failed before last fix, passes
 after it

---
 test/jalview/datamodel/AlignmentTest.java |   63 +++++++++++++++++++++++++++++
 1 file changed, 63 insertions(+)

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index 7ad9436..fcf724a 100644
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -1042,4 +1042,67 @@ public class AlignmentTest
     assertEquals(23, startEnd[1]);
   }
 
+  /**
+   * Tests that dbrefs with mappings to sequence get updated if the sequence
+   * acquires a dataset sequence
+   */
+  @Test(groups = "Functional")
+  public void testCreateDataset_updateDbrefMappings()
+  {
+    SequenceI pep = new Sequence("pep", "ASD");
+    SequenceI dna = new Sequence("dna", "aaaGCCTCGGATggg");
+    SequenceI cds = new Sequence("cds", "GCCTCGGAT");
+  
+    // add dbref from dna to peptide
+    DBRefEntry dbr = new DBRefEntry("UNIPROT", "", "pep");
+    dbr.setMap(new Mapping(pep, new MapList(new int[] { 4, 15 }, new int[] {
+        1, 4 }, 3, 1)));
+    dna.addDBRef(dbr);
+
+    // add dbref from dna to peptide
+    DBRefEntry dbr2 = new DBRefEntry("UNIPROT", "", "pep");
+    dbr2.setMap(new Mapping(pep, new MapList(new int[] { 1, 12 }, new int[]
+    { 1, 4 }, 3, 1)));
+    cds.addDBRef(dbr2);
+
+    // add dbref from peptide to dna
+    DBRefEntry dbr3 = new DBRefEntry("EMBL", "", "dna");
+    dbr3.setMap(new Mapping(dna, new MapList(new int[] { 1, 4 }, new int[] {
+        4, 15 }, 1, 3)));
+    pep.addDBRef(dbr3);
+
+    // add dbref from peptide to cds
+    DBRefEntry dbr4 = new DBRefEntry("EMBLCDS", "", "cds");
+    dbr4.setMap(new Mapping(cds, new MapList(new int[] { 1, 4 }, new int[] {
+        1, 12 }, 1, 3)));
+    pep.addDBRef(dbr4);
+
+    AlignmentI protein = new Alignment(new SequenceI[] { pep });
+  
+    /*
+     * create the alignment dataset
+     */
+    ((Alignment) protein).createDatasetAlignment();
+  
+    AlignmentI ds = protein.getDataset();
+  
+    // should be 3 sequences in dataset
+    assertEquals(3, ds.getHeight());
+    assertTrue(ds.getSequences().contains(pep.getDatasetSequence()));
+    assertTrue(ds.getSequences().contains(dna));
+    assertTrue(ds.getSequences().contains(cds));
+
+    /*
+     * verify peptide.cdsdbref.peptidedbref is now mapped to peptide dataset
+     */
+    DBRefEntry[] dbRefs = pep.getDBRefs();
+    assertEquals(2, dbRefs.length);
+    assertSame(dna, dbRefs[0].map.to);
+    assertSame(cds, dbRefs[1].map.to);
+    assertEquals(1, dna.getDBRefs().length);
+    assertSame(pep.getDatasetSequence(), dna.getDBRefs()[0].map.to);
+    assertEquals(1, cds.getDBRefs().length);
+    assertSame(pep.getDatasetSequence(), cds.getDBRefs()[0].map.to);
+  }
+
 }
-- 
1.7.10.2