From b3ab81b9e34fbb6de969ec0c3230c887661c3b48 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 8 Oct 2020 15:30:22 +0100
Subject: [PATCH] JAL-3700 JAL-3763 create datasets for test sequences

---
 test/jalview/util/MappingUtilsTest.java |   12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java
index 3c1dbbb..2fb29f1 100644
--- a/test/jalview/util/MappingUtilsTest.java
+++ b/test/jalview/util/MappingUtilsTest.java
@@ -1325,7 +1325,8 @@ public class MappingUtilsTest
   /**
    * Test mapping a sequence group where sequences in and outside the group
    * share a dataset sequence (e.g. alternative CDS for the same gene)
-   * 
+   * <p>
+   * This scenario doesn't arise after JAL-3763 changes, but test left as still valid
    * @throws IOException
    */
   @Test(groups = { "Functional" })
@@ -1347,6 +1348,9 @@ public class MappingUtilsTest
     SequenceI pep1 = new Sequence("pep1", "KF");
     SequenceI pep2 = new Sequence("pep2", "FG");
     SequenceI pep3 = new Sequence("pep3", "GP");
+    pep1.createDatasetSequence();
+    pep2.createDatasetSequence();
+    pep3.createDatasetSequence();
 
     /*
      * add mappings from coding positions of dna to respective peptides
@@ -1371,7 +1375,7 @@ public class MappingUtilsTest
             new SequenceI[]
             { pep1, pep2, pep3 });
     AlignViewportI cdnaView = new AlignViewport(cdna);
-    AlignViewportI proteinView = new AlignViewport(protein);
+    AlignViewportI peptideView = new AlignViewport(protein);
     protein.setCodonFrames(acfList);
 
     /*
@@ -1389,7 +1393,7 @@ public class MappingUtilsTest
      * Verify the mapped sequence group in dna is cds1 and cds3
      */
     SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg,
-            proteinView, cdnaView);
+            peptideView, cdnaView);
     assertTrue(mappedGroup.getColourText());
     assertSame(sg.getIdColour(), mappedGroup.getIdColour());
     assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
@@ -1408,7 +1412,7 @@ public class MappingUtilsTest
     sg.addSequence(cds1, false);
     sg.setStartRes(0);
     sg.setEndRes(cdna.getWidth() - 1);
-    mappedGroup = MappingUtils.mapSequenceGroup(sg, cdnaView, proteinView);
+    mappedGroup = MappingUtils.mapSequenceGroup(sg, cdnaView, peptideView);
     assertTrue(mappedGroup.getColourText());
     assertSame(sg.getIdColour(), mappedGroup.getIdColour());
     assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
-- 
1.7.10.2