X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignViewportTest.java;h=d6b2454c716ba86d673c8626cf996837f3d0f318;hb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;hp=b49352b6d35cdd6f0efd8df642f16979b15208a4;hpb=ab22918ab8fc67d30dad1fb1ae0f37e51f49df95;p=jalview.git

diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index b49352b..d6b2454 100644
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -1,15 +1,55 @@
+/*
+ * 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.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
 
+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.Annotation;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.PIDColourScheme;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MapList;
 
+import java.util.ArrayList;
+import java.util.List;
+
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
@@ -17,43 +57,47 @@ public class AlignViewportTest
 {
 
   AlignmentI al;
+
   AlignViewport testee;
 
-  @BeforeMethod
+  @BeforeClass(alwaysRun = true)
+  public static void setUpBeforeClass() throws Exception
+  {
+    Jalview.main(new String[] { "-props", "test/jalview/testProps.jvprops" });
+  }
+
+  @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" })
+  @Test(groups = { "Functional" })
   public void testCollateForPdb()
   {
+    // JBP: What behaviour is this supposed to test ?
     /*
      * 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"));
+            .addPDBId(new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"));
     al.getSequenceAt(2).getDatasetSequence()
-            .addPDBId(
-            new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"));
+            .addPDBId(new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"));
     al.getSequenceAt(1).getDatasetSequence()
-            .addPDBId(
-            new PDBEntry("2ABC", "C", Type.PDB, "2ABC.pdb"));
+            .addPDBId(new PDBEntry("2ABC", "C", Type.PDB, "2ABC.pdb"));
     /*
      * Add a second chain PDB xref to Seq2 - should not result in a duplicate in
      * the results
@@ -69,8 +113,8 @@ public class AlignViewportTest
     /*
      * run method under test
      */
-    SequenceI[][] seqs = testee.collateForPDB(new PDBEntry[]
-    { pdb1, pdb2, pdb3 });
+    SequenceI[][] seqs = testee.collateForPDB(new PDBEntry[] { pdb1, pdb2,
+        pdb3 });
 
     // seq1 and seq3 refer to PDBEntry[0]
     assertEquals(2, seqs[0].length);
@@ -84,4 +128,249 @@ public class AlignViewportTest
     // no sequence refers to PDBEntry[2]
     assertEquals(0, seqs[2].length);
   }
+
+  /**
+   * 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<AlignedCodonFrame>();
+    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);
+    assertEquals(2, ssm.getSequenceMappings().size());
+    assertTrue(ssm.getSequenceMappings().contains(acf1));
+    assertTrue(ssm.getSequenceMappings().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, ssm.getSequenceMappings().size());
+    assertTrue(ssm.getSequenceMappings().contains(acf1));
+    assertTrue(ssm.getSequenceMappings().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<AlignedCodonFrame>();
+    mappings1.add(acf1);
+    af1.getViewport().getAlignment().setCodonFrames(mappings1);
+
+    List<AlignedCodonFrame> mappings2 = new ArrayList<AlignedCodonFrame>();
+    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<AlignedCodonFrame>();
+    mappings1.add(acf1);
+    mappings1.add(acf2);
+    af1.getViewport().getAlignment().setCodonFrames(mappings1);
+
+    List<AlignedCodonFrame> mappings2 = new ArrayList<AlignedCodonFrame>();
+    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" })
+  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_IDENTITY",
+            Boolean.FALSE.toString());
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/uniref50.fa", DataSourceType.FILE);
+    AlignmentAnnotation[] anns = af.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);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testSetGlobalColourScheme()
+  {
+    /*
+     * test for JAL-2283 don't inadvertently turn on colour by conservation
+     */
+    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();
+    af.getViewport().setGlobalColourScheme(cs);
+    assertFalse(cs.conservationApplied());
+  }
+
+  @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());
+  }
 }