JAL-2023 fix for CDS shared dataset, robust load of split frame project

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index f2262fb..332c649 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -1302,7 +1302,9 @@ public class AlignmentUtils
 
   /**
    * Constructs an alignment consisting of the mapped exon regions in the given
-   * nucleotide sequences, and updates mappings to match.
+   * nucleotide sequences, and updates mappings to match. The new alignment's
+   * sequences are added to the parent alignment's dataset, and both alignments
+   * share the same dataset.
    * 
    * @param dna
    *          aligned dna sequences
@@ -1312,7 +1314,7 @@ public class AlignmentUtils
    *         sequences (or null if no exons are found)
    */
   public static AlignmentI makeExonAlignment(SequenceI[] dna,
-          Set<AlignedCodonFrame> mappings)
+          Set<AlignedCodonFrame> mappings, AlignmentI al)
   {
     Set<AlignedCodonFrame> newMappings = new LinkedHashSet<AlignedCodonFrame>();
     List<SequenceI> exonSequences = new ArrayList<SequenceI>();
@@ -1334,9 +1336,21 @@ public class AlignmentUtils
         }
       }
     }
-    AlignmentI al = new Alignment(
+    AlignmentI cds = new Alignment(
             exonSequences.toArray(new SequenceI[exonSequences.size()]));
-    al.setDataset(null);
+
+    /*
+     * add new sequences to the shared dataset, set it on the new alignment
+     */
+    List<SequenceI> dsseqs = al.getDataset().getSequences();
+    for (SequenceI seq : cds.getSequences())
+    {
+      if (!dsseqs.contains(seq.getDatasetSequence()))
+      {
+        dsseqs.add(seq.getDatasetSequence());
+      }
+    }
+    cds.setDataset(al.getDataset());
 
     /*
      * Replace the old mappings with the new ones
@@ -1344,7 +1358,7 @@ public class AlignmentUtils
     mappings.clear();
     mappings.addAll(newMappings);
 
-    return al;
+    return cds;
   }
 
   /**

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 63e6787..56cf231 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -845,6 +845,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * operation that affects the data in the current view (selection changed,
    * etc) to update the menus to reflect the new state.
    */
+  @Override
   public void setMenusForViewport()
   {
     setMenusFromViewport(viewport);
@@ -1401,6 +1402,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     alignPanel.makeEPS(f);
   }
 
+  @Override
   public void createSVG(File f)
   {
     alignPanel.makeSVG(f);
@@ -1574,6 +1576,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
+  @Override
   public void addHistoryItem(CommandI command)
   {
     if (command.getSize() > 0)
@@ -3497,6 +3500,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param cs
    *          DOCUMENT ME!
    */
+  @Override
   public void changeColour(ColourSchemeI cs)
   {
     // TODO: pull up to controller method
@@ -4752,8 +4756,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         try
         {
           // update our local dataset reference
-          Alignment ds = AlignFrame.this.getViewport().getAlignment()
-                  .getDataset();
+          AlignmentI alignment = AlignFrame.this.getViewport()
+                  .getAlignment();
+          Alignment ds = alignment.getDataset();
           Alignment prods = CrossRef
                   .findXrefSequences(sel, dna, source, ds);
           if (prods != null)
@@ -4806,7 +4811,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               if (dna)
               {
                 copyAlignment = AlignmentUtils.makeExonAlignment(
-                        sequenceSelection, cf);
+                        sequenceSelection, cf, alignment);
                 al.getCodonFrames().clear();
                 al.getCodonFrames().addAll(cf);
                 final StructureSelectionManager ssm = StructureSelectionManager
@@ -5755,6 +5760,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.firePropertyChange("alignment", null, al);
   }
 
+  @Override
   public void setShowSeqFeatures(boolean b)
   {
     showSeqFeatures.setSelected(b);

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 6fea041..ce8d2dd 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -163,7 +163,7 @@ public class Jalview2XML
    */
   Map<String, SequenceI> seqRefIds = null;
 
-  Vector frefedSequence = null;
+  Vector<Object[]> frefedSequence = null;
 
   boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
 
@@ -258,7 +258,7 @@ public class Jalview2XML
       int r = 0, rSize = frefedSequence.size();
       while (r < rSize)
       {
-        Object[] ref = (Object[]) frefedSequence.elementAt(r);
+        Object[] ref = frefedSequence.elementAt(r);
         if (ref != null)
         {
           String sref = (String) ref[0];
@@ -2178,6 +2178,7 @@ public class Jalview2XML
       {
         SwingUtilities.invokeAndWait(new Runnable()
         {
+          @Override
           public void run()
           {
             setLoadingFinishedForNewStructureViewers();
@@ -2252,7 +2253,7 @@ public class Jalview2XML
     }
     if (frefedSequence == null)
     {
-      frefedSequence = new Vector();
+      frefedSequence = new Vector<Object[]>();
     }
 
     AlignFrame af = null, _af = null;
@@ -2848,7 +2849,7 @@ public class Jalview2XML
             {
               mapping = addMapping(maps[m].getMapping());
             }
-            if (dnaseq != null)
+            if (dnaseq != null && mapping.getTo() != null)
             {
               cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
             }
@@ -5088,7 +5089,7 @@ public class Jalview2XML
     }
     if (this.frefedSequence == null)
     {
-      frefedSequence = new Vector();
+      frefedSequence = new Vector<Object[]>();
     }
 
     viewportsAdded.clear();

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index b13f991..febe991 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -1026,11 +1026,23 @@ public class AlignmentUtilsTests
     acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
     mappings.add(acf);
 
+    AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
+    dna.setDataset(null);
     AlignmentI exons = AlignmentUtils.makeExonAlignment(new SequenceI[] {
-        dna1, dna2 }, mappings);
-    assertEquals(2, exons.getSequences().size());
-    assertEquals("GGGTTT", exons.getSequenceAt(0).getSequenceAsString());
-    assertEquals("GGGTTTCCC", exons.getSequenceAt(1).getSequenceAsString());
+        dna1, dna2 }, mappings, dna);
+    List<SequenceI> exonSeqs = exons.getSequences();
+    assertEquals(2, exonSeqs.size());
+    assertEquals("GGGTTT", exonSeqs.get(0).getSequenceAsString());
+    assertEquals("GGGTTTCCC", exonSeqs.get(1).getSequenceAsString());
+
+    /*
+     * verify shared, extended alignment dataset
+     */
+    assertSame(dna.getDataset(), exons.getDataset());
+    assertTrue(dna.getDataset().getSequences()
+            .contains(exonSeqs.get(0).getDatasetSequence()));
+    assertTrue(dna.getDataset().getSequences()
+            .contains(exonSeqs.get(1).getDatasetSequence()));
 
     /*
      * Verify updated mappings
@@ -1183,8 +1195,10 @@ public class AlignmentUtilsTests
      * Create the Exon alignment; also replaces the dna-to-protein mappings with
      * exon-to-protein and exon-to-dna mappings
      */
+    AlignmentI dna = new Alignment(new SequenceI[] { dna1 });
+    dna.setDataset(null);
     AlignmentI exal = AlignmentUtils.makeExonAlignment(
-            new SequenceI[] { dna1 }, mappings);
+            new SequenceI[] { dna1 }, mappings, dna);
 
     /*
      * Verify we have 3 exon sequences, mapped to pep1/2/3 respectively
@@ -1192,6 +1206,17 @@ public class AlignmentUtilsTests
     List<SequenceI> exons = exal.getSequences();
     assertEquals(3, exons.size());
 
+    /*
+     * verify shared, extended alignment dataset
+     */
+    assertSame(dna.getDataset(), exal.getDataset());
+    assertTrue(dna.getDataset().getSequences()
+            .contains(exons.get(0).getDatasetSequence()));
+    assertTrue(dna.getDataset().getSequences()
+            .contains(exons.get(1).getDatasetSequence()));
+    assertTrue(dna.getDataset().getSequences()
+            .contains(exons.get(2).getDatasetSequence()));
+
     SequenceI exon = exons.get(0);
     assertEquals("GGGTTT", exon.getSequenceAsString());
     assertEquals("dna1|A12345", exon.getName());