Merge branch 'develop' into features/JAL-2110_crossRefDuplications

diff --combined test/jalview/gui/AlignViewportTest.java
index dc9113c,c956da1..2b72914
--- 1/test/jalview/gui/AlignViewportTest.java
--- 2/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@@ -36,7 -36,6 +36,7 @@@ import jalview.datamodel.SequenceI
  import jalview.io.FileLoader;
  import jalview.io.FormatAdapter;
  import jalview.structure.StructureSelectionManager;
 +import jalview.util.MapList;
  
  import java.util.ArrayList;
  import java.util.List;
@@@ -77,12 -76,12 +77,12 @@@ public class AlignViewportTes
      /*
       * Set up sequence pdb ids
       */
-     PDBEntry pdb1 = new PDBEntry("1ABC", "A", Type.PDB, "1ABC.pdb");
-     PDBEntry pdb2 = new PDBEntry("2ABC", "A", Type.PDB, "2ABC.pdb");
-     PDBEntry pdb3 = new PDBEntry("3ABC", "A", Type.PDB, "3ABC.pdb");
+     PDBEntry pdb1 = new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb");
+     PDBEntry pdb2 = new PDBEntry("2ABC", "C", Type.PDB, "2ABC.pdb");
+     PDBEntry pdb3 = new PDBEntry("3ABC", "D", Type.PDB, "3ABC.pdb");
  
      /*
-      * seq1 and seq3 refer to 1ABC, seq2 to 2ABC, none to 3ABC
+      * seq1 and seq3 refer to 1abcB, seq2 to 2abcC, none to 3abcD
       */
      al.getSequenceAt(0).getDatasetSequence()
              .addPDBId(new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"));
@@@ -134,13 -133,8 +134,13 @@@
      AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
              ">Seq1\nCAGT\n", FormatAdapter.PASTE);
  
 +    SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
      AlignedCodonFrame acf1 = new AlignedCodonFrame();
 +    acf1.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 1, 4 },
 +            1, 1));
      AlignedCodonFrame acf2 = new AlignedCodonFrame();
 +    acf2.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 4, 1 },
 +            1, 1));
  
      List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
      mappings.add(acf1);
@@@ -184,20 -178,10 +184,20 @@@
              ">Seq1\nRSVQ\n", FormatAdapter.PASTE);
      AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
              ">Seq2\nDGEL\n", FormatAdapter.PASTE);
 -
 +    SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA");
 +    SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA");
 +    SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
 +    SequenceI s2 = af2.getViewport().getAlignment().getSequenceAt(0);
 +    // need to be distinct
      AlignedCodonFrame acf1 = new AlignedCodonFrame();
 +    acf1.addMap(cs1, s1, new MapList(new int[] { 1, 4 },
 +            new int[] { 1, 12 }, 1, 3));
      AlignedCodonFrame acf2 = new AlignedCodonFrame();
 +    acf2.addMap(cs2, s2, new MapList(new int[] { 1, 4 },
 +            new int[] { 1, 12 }, 1, 3));
      AlignedCodonFrame acf3 = new AlignedCodonFrame();
 +    acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1,
 +        12 }, 1, 1));
  
      List<AlignedCodonFrame> mappings1 = new ArrayList<AlignedCodonFrame>();
      mappings1.add(acf1);
@@@ -247,20 -231,10 +247,20 @@@
              ">Seq1\nRSVQ\n", FormatAdapter.PASTE);
      AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
              ">Seq2\nDGEL\n", FormatAdapter.PASTE);
 -
 +    SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA");
 +    SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA");
 +    SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
 +    SequenceI s2 = af2.getViewport().getAlignment().getSequenceAt(0);
 +    // need to be distinct
      AlignedCodonFrame acf1 = new AlignedCodonFrame();
 +    acf1.addMap(cs1, s1, new MapList(new int[] { 1, 4 },
 +            new int[] { 1, 12 }, 1, 3));
      AlignedCodonFrame acf2 = new AlignedCodonFrame();
 +    acf2.addMap(cs2, s2, new MapList(new int[] { 1, 4 },
 +            new int[] { 1, 12 }, 1, 3));
      AlignedCodonFrame acf3 = new AlignedCodonFrame();
 +    acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1,
 +        12 }, 1, 1));
  
      List<AlignedCodonFrame> mappings1 = new ArrayList<AlignedCodonFrame>();
      mappings1.add(acf1);

diff --combined test/jalview/structure/StructureSelectionManagerTest.java
index d07f919,16f56a6..2074fb4
--- 1/test/jalview/structure/StructureSelectionManagerTest.java
--- 2/test/jalview/structure/StructureSelectionManagerTest.java
+++ b/test/jalview/structure/StructureSelectionManagerTest.java
@@@ -29,7 -29,6 +29,7 @@@ import jalview.datamodel.SequenceFeatur
  import jalview.datamodel.SequenceI;
  import jalview.io.FormatAdapter;
  import jalview.io.StructureFile;
 +import jalview.util.MapList;
  
  import java.util.ArrayList;
  import java.util.List;
@@@ -44,7 -43,7 +44,7 @@@ public class StructureSelectionManagerT
    @BeforeMethod(alwaysRun = true)
    public void setUp()
    {
-     StructureViewSettings.setShowSeqFeatures(true);
+     StructureImportSettings.setShowSeqFeatures(true);
      ssm = new StructureSelectionManager();
    }
  
@@@ -52,11 -51,7 +52,11 @@@
    public void testRegisterMapping()
    {
      AlignedCodonFrame acf1 = new AlignedCodonFrame();
 +    acf1.addMap(new Sequence("s1", "ttt"), new Sequence("p1", "p"),
 +            new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
      AlignedCodonFrame acf2 = new AlignedCodonFrame();
 +    acf2.addMap(new Sequence("s2", "ttt"), new Sequence("p2", "p"),
 +            new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
  
      ssm.registerMapping(acf1);
      assertEquals(1, ssm.getSequenceMappings().size());
@@@ -80,14 -75,8 +80,14 @@@
    public void testRegisterMappings()
    {
      AlignedCodonFrame acf1 = new AlignedCodonFrame();
 +    acf1.addMap(new Sequence("s1", "ttt"), new Sequence("p1", "p"),
 +            new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
      AlignedCodonFrame acf2 = new AlignedCodonFrame();
 +    acf2.addMap(new Sequence("s2", "ttt"), new Sequence("p2", "p"),
 +            new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
      AlignedCodonFrame acf3 = new AlignedCodonFrame();
 +    acf3.addMap(new Sequence("s3", "ttt"), new Sequence("p3", "p"),
 +            new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
  
      List<AlignedCodonFrame> set1 = new ArrayList<AlignedCodonFrame>();
      set1.add(acf1);