X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignViewportTest.java;h=959abb086155807e590011b6265180df5a9a7e90;hb=bc18effe68ba80213a6d03ca7e6175adc6be71d6;hp=812fd8ff5e6e63436f7994fce03ee6751e357237;hpb=5779b71c22d85070cbb59aa51a612d03f9744cc3;p=jalview.git

diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index 812fd8f..959abb0 100644
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -23,6 +23,7 @@ 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;
 
@@ -33,8 +34,6 @@ 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;
@@ -42,6 +41,7 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
+import jalview.schemes.ClustalxColourScheme;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.PIDColourScheme;
 import jalview.structure.StructureSelectionManager;
@@ -96,57 +96,6 @@ public class AlignViewportTest
     testee = new AlignViewport(al);
   }
 
-  @Test(groups = { "Functional" })
-  public void testCollateForPdb()
-  {
-    // JBP: What behaviour is this supposed to test ?
-    /*
-     * Set up sequence pdb ids
-     */
-    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 1abcB, seq2 to 2abcC, none to 3abcD
-     */
-    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"));
-    /*
-     * Add a second chain PDB xref to Seq2 - should not result in a duplicate in
-     * the results
-     */
-    al.getSequenceAt(1).getDatasetSequence()
-            .addPDBId(new PDBEntry("2ABC", "D", Type.PDB, "2ABC.pdb"));
-    /*
-     * Seq3 refers to 3abc - this does not match 3ABC (as the code stands)
-     */
-    al.getSequenceAt(2).getDatasetSequence()
-            .addPDBId(new PDBEntry("3abc", "D", Type.PDB, "3ABC.pdb"));
-
-    /*
-     * run method under test
-     */
-    SequenceI[][] seqs = testee.collateForPDB(new PDBEntry[] { pdb1, pdb2,
-        pdb3 });
-
-    // 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]);
-
-    // seq2 refers to PDBEntry[1]
-    assertEquals(1, seqs[1].length);
-    assertSame(al.getSequenceAt(1), seqs[1][0]);
-
-    // 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
@@ -328,7 +277,7 @@ public class AlignViewportTest
    * Test for JAL-1306 - conservation thread should run even when only Quality
    * (and not Conservation) is enabled in Preferences
    */
-  @Test(groups = { "Functional" })
+  @Test(groups = { "Functional" }, timeOut=2000)
   public void testUpdateConservation_qualityOnly()
   {
     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
@@ -343,7 +292,24 @@ public class AlignViewportTest
             Boolean.FALSE.toString());
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
-    AlignmentAnnotation[] anns = af.viewport.getAlignment()
+
+    /*
+     * wait for Conservation thread to complete
+     */
+    AlignViewport viewport = af.getViewport();
+    synchronized (this)
+    {
+      while (viewport.getAlignmentConservationAnnotation() != null)
+      {
+        try
+        {
+          wait(50);
+        } catch (InterruptedException e)
+        {
+        }
+      }
+    }
+    AlignmentAnnotation[] anns = viewport.getAlignment()
             .getAlignmentAnnotation();
     assertNotNull("No annotations found", anns);
     assertEquals("More than one annotation found", 1, anns.length);
@@ -367,9 +333,34 @@ public class AlignViewportTest
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
     ColourSchemeI cs = new PIDColourScheme();
-    af.getViewport().setGlobalColourScheme(cs);
-    assertFalse(af.getViewport().getResidueShading()
+    AlignViewport viewport = af.getViewport();
+    viewport.setGlobalColourScheme(cs);
+    assertFalse(viewport.getResidueShading()
             .conservationApplied());
+
+    /*
+     * JAL-3201 groups have their own ColourSchemeI instances
+     */
+    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" })