JAL-1369 fix bug reloading a project with group sequence reps

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 01e60d4..945651b 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -4144,25 +4144,25 @@ public class Jalview2XML
     {
       for (int s = 0; s < JSEQ.length; s++)
       {
-        jalview.datamodel.SequenceGroup hidden = new jalview.datamodel.SequenceGroup();
-
+        SequenceGroup hidden = new SequenceGroup();
+        boolean isRepresentative = false;
         for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
         {
-          hidden.addSequence(
-                  al.getSequenceAt(JSEQ[s].getHiddenSequences(r)), false);
+          isRepresentative = true;
+          SequenceI sequenceToHide = al.getSequenceAt(JSEQ[s]
+                  .getHiddenSequences(r));
+          hidden.addSequence(sequenceToHide, false);
+          // remove from hiddenSeqs list so we don't try to hide it twice
+          hiddenSeqs.remove(sequenceToHide);
+        }
+        if (isRepresentative)
+        {
+          SequenceI representativeSequence = al.getSequenceAt(s);
+          hidden.addSequence(representativeSequence, false);
+          af.viewport.hideRepSequences(representativeSequence, hidden);
         }
-        af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
       }
 
-      // jalview.datamodel.SequenceI[] hseqs = new
-      // jalview.datamodel.SequenceI[hiddenSeqs
-      // .size()];
-      //
-      // for (int s = 0; s < hiddenSeqs.size(); s++)
-      // {
-      // hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
-      // }
-
       SequenceI[] hseqs = hiddenSeqs.toArray(new SequenceI[hiddenSeqs
               .size()]);
       af.viewport.hideSequence(hseqs);

diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java
index a77e10a..38153df 100644 (file)
--- a/test/jalview/io/Jalview2xmlTests.java
+++ b/test/jalview/io/Jalview2xmlTests.java
@@ -22,6 +22,8 @@ package jalview.io;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.api.AlignViewportI;
@@ -31,6 +33,7 @@ import jalview.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenSequences;
+import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
@@ -437,12 +440,8 @@ public class Jalview2xmlTests
     assertTrue("Didn't read in the example file correctly.", af != null);
     String afid = af.getViewport().getSequenceSetId();
 
-    /*
-     * remember representative and hidden sequences marked 
-     * on each panel
-     */
+    // remember reference sequence for each panel
     Map<String, SequenceI> refseqs = new HashMap<String, SequenceI>();
-    Map<String, List<String>> hiddenSeqNames = new HashMap<String, List<String>>();
 
     /*
      * mark sequence 2, 3, 4.. in panels 1, 2, 3...
@@ -456,31 +455,7 @@ public class Jalview2xmlTests
       int repIndex = n % alignment.getHeight();
       SequenceI rep = alignment.getSequenceAt(repIndex);
       refseqs.put(ap.getViewName(), rep);
-      List<String> hiddenNames = new ArrayList<String>();
-      hiddenSeqNames.put(ap.getViewName(), hiddenNames);
-
-      /*
-       * hide rep sequence and the one before it
-       */
-      SequenceI seqToHide = alignment.getSequenceAt(repIndex);
-      SequenceGroup sg = new SequenceGroup();
-      sg.addSequence(seqToHide, false);
-      SequenceI precedingSeq = alignment.getSequenceAt(repIndex - 1);
-      sg.addSequence(precedingSeq, false);
-      av.setSelectionGroup(sg);
-      ((AlignmentViewport) av).hideSequences(seqToHide, true);
 
-      /*
-       * record names of hidden sequences
-       */
-      HiddenSequences hs = alignment.getHiddenSequences();
-      for (SequenceI seq : hs.hiddenSequences)
-      {
-        if (seq != null)
-        {
-          hiddenNames.add(seq.getName());
-        }
-      }
       // code from mark/unmark sequence as reference in jalview.gui.PopupMenu
       // todo refactor this to an alignment view controller
       av.setDisplayReferenceSeq(true);
@@ -526,16 +501,6 @@ public class Jalview2xmlTests
               "Display reference sequence view setting not set.");
       Assert.assertTrue(ap.getAlignViewport().isColourByReferenceSeq(),
               "Colour By Reference Seq view setting not set.");
-
-      /*
-       * verify hidden sequences in restored panel
-       */
-      List<String> hidden = hiddenSeqNames.get(ap.getViewName());
-      HiddenSequences hs = alignment.getHiddenSequences();
-      assertEquals(
-              "wrong number of restored hidden sequences in "
-                      + ap.getViewName(),
-              hidden.size(), hs.getSize());
     }
   }
 
@@ -592,4 +557,126 @@ public class Jalview2xmlTests
     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.2b1"));
     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.0b2", "2.8.0b1"));
   }
+
+  /**
+   * Test save and reload of a project with a different sequence group (and
+   * representative sequence) in each view.
+   * 
+   * @throws Exception
+   */
+  @Test(groups = { "Functional" })
+  public void testStoreAndRecoverGroupRepSeqs() throws Exception
+  {
+    Desktop.instance.closeAll_actionPerformed(null);
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/uniref50.fa", FormatAdapter.FILE);
+    assertTrue("Didn't read in the example file correctly.", af != null);
+    String afid = af.getViewport().getSequenceSetId();
+    // make a second view of the alignment
+    af.newView_actionPerformed(null);
+  
+    /*
+     * remember representative and hidden sequences marked 
+     * on each panel
+     */
+    Map<String, SequenceI> repSeqs = new HashMap<String, SequenceI>();
+    Map<String, List<String>> hiddenSeqNames = new HashMap<String, List<String>>();
+  
+    /*
+     * mark sequence 2, 3, 4.. in panels 1, 2, 3...
+     * as reference sequence for itself and the preceding sequence
+     */
+    int n = 1;
+    for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
+    {
+      AlignViewportI av = ap.getAlignViewport();
+      AlignmentI alignment = ap.getAlignment();
+      int repIndex = n % alignment.getHeight();
+      // ensure at least one preceding sequence i.e. index >= 1
+      repIndex = Math.max(repIndex, 1);
+      SequenceI repSeq = alignment.getSequenceAt(repIndex);
+      repSeqs.put(ap.getViewName(), repSeq);
+      List<String> hiddenNames = new ArrayList<String>();
+      hiddenSeqNames.put(ap.getViewName(), hiddenNames);
+  
+      /*
+       * have rep sequence represent itself and the one before it
+       * this hides the group (except for the rep seq)
+       */
+      SequenceGroup sg = new SequenceGroup();
+      sg.addSequence(repSeq, false);
+      SequenceI precedingSeq = alignment.getSequenceAt(repIndex - 1);
+      sg.addSequence(precedingSeq, false);
+      sg.setSeqrep(repSeq);
+      assertTrue(sg.getSequences().contains(repSeq));
+      assertTrue(sg.getSequences().contains(precedingSeq));
+      av.setSelectionGroup(sg);
+      assertSame(repSeq, sg.getSeqrep());
+
+      /*
+       * represent group with sequence adds to a map of hidden rep sequences
+       * (it does not create a group on the alignment) 
+       */
+      ((AlignmentViewport) av).hideSequences(repSeq, true);
+      assertSame(repSeq, sg.getSeqrep());
+      assertTrue(sg.getSequences().contains(repSeq));
+      assertTrue(sg.getSequences().contains(precedingSeq));
+      assertTrue("alignment has groups", alignment.getGroups().isEmpty());
+      Map<SequenceI, SequenceCollectionI> hiddenRepSeqsMap = av.getHiddenRepSequences();
+      assertNotNull(hiddenRepSeqsMap);
+      assertEquals(1, hiddenRepSeqsMap.size());
+      assertSame(sg, hiddenRepSeqsMap.get(repSeq));
+      assertTrue(alignment.getHiddenSequences().isHidden(precedingSeq));
+      assertFalse(alignment.getHiddenSequences().isHidden(repSeq));
+      hiddenNames.add(precedingSeq.getName());
+
+      n++;
+    }
+    File tfile = File
+            .createTempFile("testStoreAndRecoverGroupReps",
+            ".jvp");
+    try
+    {
+      new Jalview2XML(false).saveState(tfile);
+    } catch (Throwable e)
+    {
+      Assert.fail("Didn't save the expanded view state", e);
+    }
+    Desktop.instance.closeAll_actionPerformed(null);
+    if (Desktop.getAlignFrames() != null)
+    {
+      Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+    }
+  
+    af = new FileLoader().LoadFileWaitTillLoaded(
+            tfile.getAbsolutePath(), FormatAdapter.FILE);
+    afid = af.getViewport().getSequenceSetId();
+  
+    for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
+    {
+      String viewName = ap.getViewName();
+      AlignViewportI av = ap.getAlignViewport();
+      AlignmentI alignment = ap.getAlignment();
+      List<SequenceGroup> groups = alignment.getGroups();
+      assertNotNull(groups);
+      assertTrue("Alignment has groups", groups.isEmpty());
+      Map<SequenceI, SequenceCollectionI> hiddenRepSeqsMap = av
+              .getHiddenRepSequences();
+      assertNotNull("No hidden represented sequences", hiddenRepSeqsMap);
+      assertEquals(1, hiddenRepSeqsMap.size());
+      assertEquals(repSeqs.get(viewName).getDisplayId(true),
+              hiddenRepSeqsMap.keySet().iterator().next()
+                      .getDisplayId(true));
+
+      /*
+       * verify hidden sequences in restored panel
+       */
+      List<String> hidden = hiddenSeqNames.get(ap.getViewName());
+      HiddenSequences hs = alignment.getHiddenSequences();
+      assertEquals(
+              "wrong number of restored hidden sequences in "
+                      + ap.getViewName(),
+              hidden.size(), hs.getSize());
+    }
+  }
 }