From b59e6ecc36fb98f4285213a685d0546e98ebd556 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 22 Oct 2020 14:48:25 +0100
Subject: [PATCH] JAL-3763 Javadoc, check for null, additional tests

---
 src/jalview/datamodel/AlignedCodonFrame.java      |    6 +-
 src/jalview/gui/PopupMenu.java                    |    7 ++-
 test/jalview/datamodel/AlignedCodonFrameTest.java |   63 +++++++++++++++++++++
 3 files changed, 72 insertions(+), 4 deletions(-)

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index 049a5f4..6faf7a6 100644
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -954,9 +954,9 @@ public class AlignedCodonFrame
   }
 
   /**
-   * Returns the first mapping found which is between the given sequence and
-   * another, is a triplet mapping (3:1 or 1:3), and covers the full extent of
-   * both sequences involved.
+   * Returns the first mapping found which is between the given dataset sequence
+   * and another, is a triplet mapping (3:1 or 1:3), and covers the full extent
+   * of both sequences involved
    * 
    * @param seq
    * @return
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 568f7f1..fc3c342 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -832,8 +832,13 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
        * show local rather than linked feature coordinates
        */
       int[] beginRange = mf.getMappedPositions(start, start);
-      start = beginRange[0];
       int[] endRange = mf.getMappedPositions(end, end);
+      if (beginRange == null || endRange == null)
+      {
+        // e.g. variant extending to stop codon so not mappable
+        return;
+      }
+      start = beginRange[0];
       end = endRange[endRange.length - 1];
     }
     StringBuilder desc = new StringBuilder();
diff --git a/test/jalview/datamodel/AlignedCodonFrameTest.java b/test/jalview/datamodel/AlignedCodonFrameTest.java
index 0cfc380..337ac1a 100644
--- a/test/jalview/datamodel/AlignedCodonFrameTest.java
+++ b/test/jalview/datamodel/AlignedCodonFrameTest.java
@@ -648,4 +648,67 @@ public class AlignedCodonFrameTest
     expected.addResult(dna1.getDatasetSequence(),  17, 18);
     assertEquals(sr, expected);
   }
+
+  @Test(groups = { "Functional" })
+  public void testGetCoveringCodonMapping()
+  {
+    SequenceI dna = new Sequence("dna/10-30", "acttcaATGGCGGACtaattt");
+    // CDS sequence with its own dataset sequence (JAL-3763)
+    SequenceI cds = new Sequence("cds/1-9", "-A--TGGC-GGAC");
+    cds.createDatasetSequence();
+    SequenceI pep = new Sequence("pep/1-3", "MAD");
+    
+    /*
+     * with null argument or no mappings
+     */
+    AlignedCodonFrame acf = new AlignedCodonFrame();
+    assertNull(acf.getCoveringCodonMapping(null));
+    assertNull(acf.getCoveringCodonMapping(dna));
+    assertNull(acf.getCoveringCodonMapping(pep));
+  
+    /*
+     * with a non-covering mapping e.g. overlapping exon
+     */
+    MapList map = new MapList(new int[] { 16, 18 }, new int[] {
+        1, 1 }, 3, 1);
+    acf.addMap(dna, pep, map);
+    assertNull(acf.getCoveringCodonMapping(dna));
+    assertNull(acf.getCoveringCodonMapping(pep));
+    
+    acf = new AlignedCodonFrame();
+    MapList map2 = new MapList(new int[] { 13, 18 }, new int[] {
+        2, 2 }, 3, 1);
+    acf.addMap(dna, pep, map2);
+    assertNull(acf.getCoveringCodonMapping(dna));
+    assertNull(acf.getCoveringCodonMapping(pep));
+    
+    /*
+     * with a covering mapping from CDS (dataset) to protein
+     */
+    acf = new AlignedCodonFrame();
+    MapList map3 = new MapList(new int[] { 1, 9 }, new int[] {
+        1, 3 }, 3, 1);
+    acf.addMap(cds.getDatasetSequence(), pep, map3);
+    assertNull(acf.getCoveringCodonMapping(dna));
+    SequenceToSequenceMapping mapping = acf.getCoveringCodonMapping(pep);
+    assertNotNull(mapping);
+    SequenceToSequenceMapping mapping2 = acf.getCoveringCodonMapping(cds.getDatasetSequence());
+    assertSame(mapping, mapping2);
+    
+    /*
+     * with a mapping that extends to stop codon
+     * (EMBL CDS location often includes the stop codon)
+     * - getCoveringCodonMapping is lenient (doesn't require exact length match)
+     */
+    SequenceI cds2 = new Sequence("cds/1-12", "-A--TGGC-GGACTAA");
+    cds2.createDatasetSequence();
+    acf = new AlignedCodonFrame();
+    MapList map4 = new MapList(new int[] { 1, 12 }, new int[] {
+        1, 3 }, 3, 1);
+    acf.addMap(cds2, pep, map4);
+    mapping = acf.getCoveringCodonMapping(cds2.getDatasetSequence());
+    assertNotNull(mapping);
+    mapping2 = acf.getCoveringCodonMapping(pep);
+    assertSame(mapping, mapping2);
+  }
 }
-- 
1.7.10.2