X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fgui%2FAlignViewportTest.java;h=b3c6b2ae1fb9fbe92c5ce1e03c8aa3ecc3c4d9db;hb=986834f1db7bd344d067bb450970578acb32c10f;hp=4c553862a2b6a0103d12f6ee3cb3c1338d60dde8;hpb=28fda83cbef0c9c82cd09a343af4e1721085c104;p=jalview.git

diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index 4c55386..b3c6b2a 100644
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -1,87 +1,540 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.gui;
 
 import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertNotSame;
 import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
 
+import java.util.ArrayList;
+import java.util.List;
+
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
+import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+import jalview.schemes.ClustalxColourScheme;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.PIDColourScheme;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MapList;
+import jalview.viewmodel.ViewportRanges;
 
 public class AlignViewportTest
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   AlignmentI al;
+
   AlignViewport testee;
 
- @BeforeMethod(alwaysRun = true)
+  @BeforeClass(alwaysRun = true)
+  public static void setUpBeforeClass() throws Exception
+  {
+    Jalview.main(
+            new String[]
+            { "-nonews", "-props", "test/jalview/testProps.jvprops" });
+
+    /*
+     * remove any sequence mappings left lying around by other tests
+     */
+    StructureSelectionManager ssm = StructureSelectionManager
+            .getStructureSelectionManager(Desktop.instance);
+    ssm.resetAll();
+  }
+
+  @BeforeMethod(alwaysRun = true)
   public void setUp()
   {
     SequenceI seq1 = new Sequence("Seq1", "ABC");
     SequenceI seq2 = new Sequence("Seq2", "ABC");
     SequenceI seq3 = new Sequence("Seq3", "ABC");
-    SequenceI[] seqs = new SequenceI[]
-    { seq1, seq2, seq3 };
+    SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3 };
     al = new Alignment(seqs);
     al.setDataset(null);
     testee = new AlignViewport(al);
   }
 
-  @Test(groups ={ "Functional" })
-  public void testCollateForPdb()
+  /**
+   * Test that a mapping is not deregistered when a second view is closed but
+   * the first still holds a reference to the mapping
+   */
+  @Test(groups = { "Functional" })
+  public void testDeregisterMapping_onCloseView()
+  {
+    /*
+     * alignment with reference to mappings
+     */
+    AlignFrame af1 = new FileLoader()
+            .LoadFileWaitTillLoaded(">Seq1\nCAGT\n", DataSourceType.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<>();
+    mappings.add(acf1);
+    mappings.add(acf2);
+    af1.getViewport().getAlignment().setCodonFrames(mappings);
+    af1.newView_actionPerformed(null);
+
+    /*
+     * Verify that creating the alignment for the new View has registered the
+     * mappings
+     */
+    StructureSelectionManager ssm = StructureSelectionManager
+            .getStructureSelectionManager(Desktop.instance);
+    List<AlignedCodonFrame> sequenceMappings = ssm.getSequenceMappings();
+    assertEquals(2, sequenceMappings.size());
+    assertTrue(sequenceMappings.contains(acf1));
+    assertTrue(sequenceMappings.contains(acf2));
+
+    /*
+     * Close the second view. Verify that mappings are not removed as the first
+     * view still holds a reference to them.
+     */
+    af1.closeMenuItem_actionPerformed(false);
+    assertEquals(2, sequenceMappings.size());
+    assertTrue(sequenceMappings.contains(acf1));
+    assertTrue(sequenceMappings.contains(acf2));
+  }
+
+  /**
+   * Test that a mapping is deregistered if no alignment holds a reference to it
+   */
+  @Test(groups = { "Functional" })
+  public void testDeregisterMapping_withNoReference()
+  {
+    Desktop d = Desktop.instance;
+    assertNotNull(d);
+    StructureSelectionManager ssm = StructureSelectionManager
+            .getStructureSelectionManager(Desktop.instance);
+    ssm.resetAll();
+
+    AlignFrame af1 = new FileLoader()
+            .LoadFileWaitTillLoaded(">Seq1\nRSVQ\n", DataSourceType.PASTE);
+    AlignFrame af2 = new FileLoader()
+            .LoadFileWaitTillLoaded(">Seq2\nDGEL\n", DataSourceType.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<>();
+    mappings1.add(acf1);
+    af1.getViewport().getAlignment().setCodonFrames(mappings1);
+
+    List<AlignedCodonFrame> mappings2 = new ArrayList<>();
+    mappings2.add(acf2);
+    mappings2.add(acf3);
+    af2.getViewport().getAlignment().setCodonFrames(mappings2);
+
+    /*
+     * AlignFrame1 has mapping acf1, AlignFrame2 has acf2 and acf3
+     */
+
+    List<AlignedCodonFrame> ssmMappings = ssm.getSequenceMappings();
+    assertEquals(0, ssmMappings.size());
+    ssm.registerMapping(acf1);
+    assertEquals(1, ssmMappings.size());
+    ssm.registerMapping(acf2);
+    assertEquals(2, ssmMappings.size());
+    ssm.registerMapping(acf3);
+    assertEquals(3, ssmMappings.size());
+
+    /*
+     * Closing AlignFrame2 should remove its mappings from
+     * StructureSelectionManager, since AlignFrame1 has no reference to them
+     */
+    af2.closeMenuItem_actionPerformed(true);
+    assertEquals(1, ssmMappings.size());
+    assertTrue(ssmMappings.contains(acf1));
+  }
+
+  /**
+   * Test that a mapping is not deregistered if another alignment holds a
+   * reference to it
+   */
+  @Test(groups = { "Functional" })
+  public void testDeregisterMapping_withReference()
+  {
+    Desktop d = Desktop.instance;
+    assertNotNull(d);
+    StructureSelectionManager ssm = StructureSelectionManager
+            .getStructureSelectionManager(Desktop.instance);
+    ssm.resetAll();
+
+    AlignFrame af1 = new FileLoader()
+            .LoadFileWaitTillLoaded(">Seq1\nRSVQ\n", DataSourceType.PASTE);
+    AlignFrame af2 = new FileLoader()
+            .LoadFileWaitTillLoaded(">Seq2\nDGEL\n", DataSourceType.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<>();
+    mappings1.add(acf1);
+    mappings1.add(acf2);
+    af1.getViewport().getAlignment().setCodonFrames(mappings1);
+
+    List<AlignedCodonFrame> mappings2 = new ArrayList<>();
+    mappings2.add(acf2);
+    mappings2.add(acf3);
+    af2.getViewport().getAlignment().setCodonFrames(mappings2);
+
+    /*
+     * AlignFrame1 has mappings acf1 and acf2, AlignFrame2 has acf2 and acf3
+     */
+
+    List<AlignedCodonFrame> ssmMappings = ssm.getSequenceMappings();
+    assertEquals(0, ssmMappings.size());
+    ssm.registerMapping(acf1);
+    assertEquals(1, ssmMappings.size());
+    ssm.registerMapping(acf2);
+    assertEquals(2, ssmMappings.size());
+    ssm.registerMapping(acf3);
+    assertEquals(3, ssmMappings.size());
+
+    /*
+     * Closing AlignFrame2 should remove mapping acf3 from
+     * StructureSelectionManager, but not acf2, since AlignFrame1 still has a
+     * reference to it
+     */
+    af2.closeMenuItem_actionPerformed(true);
+    assertEquals(2, ssmMappings.size());
+    assertTrue(ssmMappings.contains(acf1));
+    assertTrue(ssmMappings.contains(acf2));
+    assertFalse(ssmMappings.contains(acf3));
+  }
+
+  /**
+   * Test for JAL-1306 - conservation thread should run even when only Quality
+   * (and not Conservation) is enabled in Preferences
+   */
+  @Test(groups = { "Functional" }, timeOut = 2000)
+  public void testUpdateConservation_qualityOnly()
   {
+    Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
+            Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty("SHOW_QUALITY",
+            Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+            Boolean.FALSE.toString());
+    Cache.applicationProperties.setProperty("SHOW_OCCUPANCY",
+            Boolean.FALSE.toString());
+    Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+            Boolean.FALSE.toString());
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/uniref50.fa", DataSourceType.FILE);
+
     /*
-     * Set up sequence pdb ids
+     * wait for Conservation thread to complete
      */
-    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");
+    AlignViewport viewport = af.getViewport();
+    waitForCalculations(viewport);
+    AlignmentAnnotation[] anns = viewport.getAlignment()
+            .getAlignmentAnnotation();
+    assertNotNull("No annotations found", anns);
+    assertEquals("More than one annotation found", 1, anns.length);
+    assertTrue("Annotation is not Quality",
+            anns[0].description.startsWith("Alignment Quality"));
+    Annotation[] annotations = anns[0].annotations;
+    assertNotNull("Quality annotations are null", annotations);
+    assertNotNull("Quality in column 1 is null", annotations[0]);
+    assertTrue("No quality value in column 1", annotations[0].value > 10f);
+  }
 
+  /**
+   * Wait for consensus etc calculation threads to complete
+   * 
+   * @param viewport
+   */
+  protected void waitForCalculations(AlignViewport viewport)
+  {
+    synchronized (this)
+    {
+      do
+      {
+        try
+        {
+          wait(50);
+        } catch (InterruptedException e)
+        {
+        }
+      } while (viewport.getCalcManager().isWorking());
+    }
+  }
+
+  @Test(groups = { "Functional" })
+  public void testSetGlobalColourScheme()
+  {
     /*
-     * seq1 and seq3 refer to 1ABC, seq2 to 2ABC, none to 3ABC
+     * test for JAL-2283: don't inadvertently turn on colour by conservation
      */
-    al.getSequenceAt(0).getDatasetSequence()
-            .addPDBId(
-            new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"));
-    al.getSequenceAt(2).getDatasetSequence()
-            .addPDBId(
-            new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"));
-    al.getSequenceAt(1).getDatasetSequence()
-            .addPDBId(
-            new PDBEntry("2ABC", "C", Type.PDB, "2ABC.pdb"));
+    Cache.applicationProperties.setProperty("DEFAULT_COLOUR_PROT", "None");
+    Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+            Boolean.TRUE.toString());
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/uniref50.fa", DataSourceType.FILE);
+    ColourSchemeI cs = new PIDColourScheme();
+    AlignViewport viewport = af.getViewport();
+    viewport.setGlobalColourScheme(cs);
+    assertFalse(viewport.getResidueShading().conservationApplied());
+
     /*
-     * Add a second chain PDB xref to Seq2 - should not result in a duplicate in
-     * the results
+     * JAL-3201 groups have their own ColourSchemeI instances
      */
-    al.getSequenceAt(1).getDatasetSequence()
-            .addPDBId(new PDBEntry("2ABC", "D", Type.PDB, "2ABC.pdb"));
+    AlignmentI aln = viewport.getAlignment();
+    SequenceGroup sg1 = new SequenceGroup();
+    sg1.addSequence(aln.getSequenceAt(0), false);
+    sg1.addSequence(aln.getSequenceAt(2), false);
+    SequenceGroup sg2 = new SequenceGroup();
+    sg2.addSequence(aln.getSequenceAt(1), false);
+    sg2.addSequence(aln.getSequenceAt(3), false);
+    aln.addGroup(sg1);
+    aln.addGroup(sg2);
+    viewport.setColourAppliesToAllGroups(true);
+    viewport.setGlobalColourScheme(new ClustalxColourScheme());
+    ColourSchemeI cs0 = viewport.getGlobalColourScheme();
+    ColourSchemeI cs1 = sg1.getColourScheme();
+    ColourSchemeI cs2 = sg2.getColourScheme();
+    assertTrue(cs0 instanceof ClustalxColourScheme);
+    assertTrue(cs1 instanceof ClustalxColourScheme);
+    assertTrue(cs2 instanceof ClustalxColourScheme);
+    assertNotSame(cs0, cs1);
+    assertNotSame(cs0, cs2);
+    assertNotSame(cs1, cs2);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testSetGetHasSearchResults()
+  {
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/uniref50.fa", DataSourceType.FILE);
+    SearchResultsI sr = new SearchResults();
+    SequenceI s1 = af.getViewport().getAlignment().getSequenceAt(0);
+
+    // create arbitrary range on first sequence
+    sr.addResult(s1, s1.getStart() + 10, s1.getStart() + 15);
+
+    // test set
+    af.getViewport().setSearchResults(sr);
+    // has -> true
+    assertTrue(af.getViewport().hasSearchResults());
+    // get == original
+    assertEquals(sr, af.getViewport().getSearchResults());
+
+    // set(null) results in has -> false
+
+    af.getViewport().setSearchResults(null);
+    assertFalse(af.getViewport().hasSearchResults());
+  }
+
+  /**
+   * Verify that setting the selection group has the side-effect of setting the
+   * context on the group, unless it already has one, but does not change
+   * whether the group is defined or not.
+   */
+  @Test(groups = { "Functional" })
+  public void testSetSelectionGroup()
+  {
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/uniref50.fa", DataSourceType.FILE);
+    AlignViewport av = af.getViewport();
+    SequenceGroup sg1 = new SequenceGroup();
+    SequenceGroup sg2 = new SequenceGroup();
+    SequenceGroup sg3 = new SequenceGroup();
+
+    av.setSelectionGroup(sg1);
+    assertSame(sg1.getContext(), av.getAlignment()); // context set
+    assertFalse(sg1.isDefined()); // group not defined
+
+    sg2.setContext(sg1, false);
+    av.setSelectionGroup(sg2);
+    assertFalse(sg2.isDefined()); // unchanged
+    assertSame(sg2.getContext(), sg1); // unchanged
+
+    // create a defined group
+    sg3.setContext(av.getAlignment(), true);
+    av.setSelectionGroup(sg3);
+    assertTrue(sg3.isDefined()); // unchanged
+  }
+
+  /**
+   * Verify that setting/clearing SHOW_OCCUPANCY preference adds or omits
+   * occupancy row from viewport
+   */
+  @Test(groups = { "Functional" })
+  public void testShowOrDontShowOccupancy()
+  {
+    // disable occupancy
+    jalview.bin.Cache.setProperty("SHOW_OCCUPANCY",
+            Boolean.FALSE.toString());
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/uniref50.fa", DataSourceType.FILE);
+    AlignViewport av = af.getViewport();
+    Assert.assertNull(av.getAlignmentGapAnnotation(),
+            "Preference did not disable occupancy row.");
+    int c = 0;
+    for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
+            null, "Occupancy"))
+    {
+      c++;
+    }
+    Assert.assertEquals(c, 0, "Expected zero occupancy rows.");
+
+    // enable occupancy
+    jalview.bin.Cache.setProperty("SHOW_OCCUPANCY",
+            Boolean.TRUE.toString());
+    af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
+            DataSourceType.FILE);
+    av = af.getViewport();
+    Assert.assertNotNull(av.getAlignmentGapAnnotation(),
+            "Preference did not enable occupancy row.");
+    c = 0;
+    for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
+            null, av.getAlignmentGapAnnotation().label))
+    {
+      c++;
+    }
+    ;
+    Assert.assertEquals(c, 1, "Expected to find one occupancy row.");
+  }
+
+  @Test(groups = { "Functional" })
+  public void testGetConsensusSeq()
+  {
     /*
-     * Seq3 refers to 3abc - this does not match 3ABC (as the code stands)
+     * A-C
+     * A-C
+     * A-D
+     * --D
+     * consensus expected to be A-C
      */
-    al.getSequenceAt(2).getDatasetSequence()
-            .addPDBId(new PDBEntry("3abc", "D", Type.PDB, "3ABC.pdb"));
+    String fasta = ">s1\nA-C\n>s2\nA-C\n>s3\nA-D\n>s4\n--D\n";
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fasta,
+            DataSourceType.PASTE);
+    AlignViewport testme = af.getViewport();
+    waitForCalculations(testme);
+    SequenceI cons = testme.getConsensusSeq();
+    assertEquals("A-C", cons.getSequenceAsString());
+  }
+
+  @Test(groups = { "Functional" })
+  public void testHideRevealSequences()
+  {
+    ViewportRanges ranges = testee.getRanges();
+    assertEquals(3, al.getHeight());
+    assertEquals(0, ranges.getStartSeq());
+    assertEquals(2, ranges.getEndSeq());
 
     /*
-     * run method under test
+     * hide first sequence
      */
-    SequenceI[][] seqs = testee.collateForPDB(new PDBEntry[]
-    { pdb1, pdb2, pdb3 });
+    testee.hideSequence(new SequenceI[] { al.getSequenceAt(0) });
+    assertEquals(2, al.getHeight());
+    assertEquals(0, ranges.getStartSeq());
+    assertEquals(1, ranges.getEndSeq());
 
-    // seq1 and seq3 refer to PDBEntry[0]
-    assertEquals(2, seqs[0].length);
-    assertSame(al.getSequenceAt(0), seqs[0][0]);
-    assertSame(al.getSequenceAt(2), seqs[0][1]);
+    /*
+     * reveal hidden sequences above the first
+     */
+    testee.showSequence(0);
+    assertEquals(3, al.getHeight());
+    assertEquals(0, ranges.getStartSeq());
+    assertEquals(2, ranges.getEndSeq());
 
-    // seq2 refers to PDBEntry[1]
-    assertEquals(1, seqs[1].length);
-    assertSame(al.getSequenceAt(1), seqs[1][0]);
+    /*
+     * hide first and third sequences
+     */
+    testee.hideSequence(
+            new SequenceI[]
+            { al.getSequenceAt(0), al.getSequenceAt(2) });
+    assertEquals(1, al.getHeight());
+    assertEquals(0, ranges.getStartSeq());
+    assertEquals(0, ranges.getEndSeq());
 
-    // no sequence refers to PDBEntry[2]
-    assertEquals(0, seqs[2].length);
+    /*
+     * reveal all hidden sequences
+     */
+    testee.showAllHiddenSeqs();
+    assertEquals(3, al.getHeight());
+    assertEquals(0, ranges.getStartSeq());
+    assertEquals(2, ranges.getEndSeq());
   }
 }