X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignFrameTest.java;h=3e82547e7ab30739f863ebdee26b148fc437920d;hb=6f812eb434553c97cccaaaefa35da54afc72bb79;hp=2ea94a4d567d21dabd458e9b7751b6869aeb2af4;hpb=4f094851cd2247ea2d982e7829a6f5b663042573;p=jalview.git

diff --git a/test/jalview/gui/AlignFrameTest.java b/test/jalview/gui/AlignFrameTest.java
index 2ea94a4..3e82547 100644
--- a/test/jalview/gui/AlignFrameTest.java
+++ b/test/jalview/gui/AlignFrameTest.java
@@ -20,25 +20,29 @@
  */
 package jalview.gui;
 
+import static org.junit.Assert.assertNotEquals;
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertFalse;
 import static org.testng.Assert.assertNotSame;
 import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 
+import jalview.api.FeatureColourI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
-import jalview.io.Jalview2xmlTests;
+import jalview.project.Jalview2xmlTests;
 import jalview.renderer.ResidueShaderI;
 import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.FeatureColour;
 import jalview.schemes.HelixColourScheme;
 import jalview.schemes.JalviewColourScheme;
 import jalview.schemes.StrandColourScheme;
@@ -46,7 +50,7 @@ import jalview.schemes.TurnColourScheme;
 import jalview.util.MessageManager;
 
 import java.awt.Color;
-import java.util.List;
+import java.util.Iterator;
 
 import org.testng.annotations.AfterMethod;
 import org.testng.annotations.BeforeClass;
@@ -58,66 +62,9 @@ public class AlignFrameTest
   AlignFrame af;
 
   @BeforeClass(alwaysRun = true)
-  public void setUpJvOptionPane()
-  {
-    JvOptionPane.setInteractiveMode(false);
-    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
-  }
-
-  @Test(groups = "Functional")
-  public void testHideFeatureColumns()
-  {
-    SequenceI seq1 = new Sequence("Seq1", "ABCDEFGHIJ");
-    SequenceI seq2 = new Sequence("Seq2", "ABCDEFGHIJ");
-    seq1.addSequenceFeature(new SequenceFeature("Metal", "", 1, 5,
-            Float.NaN, null));
-    seq2.addSequenceFeature(new SequenceFeature("Metal", "", 6, 10,
-            Float.NaN, null));
-    seq1.addSequenceFeature(new SequenceFeature("Turn", "", 2, 4,
-            Float.NaN, null));
-    seq2.addSequenceFeature(new SequenceFeature("Turn", "", 7, 9,
-            Float.NaN, null));
-    AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
-    AlignFrame alignFrame = new AlignFrame(al, al.getWidth(), al.getHeight());
-
-    /*
-     * hiding a feature not present does nothing
-     */
-    assertFalse(alignFrame.hideFeatureColumns("exon", true));
-    assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
-    assertTrue(alignFrame.getViewport().getColumnSelection().getHiddenColumns()
-            .isEmpty());
-    assertFalse(alignFrame.hideFeatureColumns("exon", false));
-    assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
-    assertTrue(alignFrame.getViewport().getColumnSelection().getHiddenColumns()
-            .isEmpty());
-
-    /*
-     * hiding a feature in all columns does nothing
-     */
-    assertFalse(alignFrame.hideFeatureColumns("Metal", true));
-    assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
-    List<int[]> hidden = alignFrame.getViewport().getColumnSelection()
-            .getHiddenColumns();
-    assertTrue(hidden.isEmpty());
-
-    /*
-     * hide a feature present in some columns
-     * sequence positions [2-4], [7-9] are column positions
-     * [1-3], [6-8] base zero
-     */
-    assertTrue(alignFrame.hideFeatureColumns("Turn", true));
-    hidden = alignFrame.getViewport().getColumnSelection().getHiddenColumns();
-    assertEquals(hidden.size(), 2);
-    assertEquals(hidden.get(0)[0], 1);
-    assertEquals(hidden.get(0)[1], 3);
-    assertEquals(hidden.get(1)[0], 6);
-    assertEquals(hidden.get(1)[1], 8);
-  }
-
-  @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
+    setUpJvOptionPane();
     /*
      * use read-only test properties file
      */
@@ -132,8 +79,8 @@ public class AlignFrameTest
   }
 
   /**
-   * configure (read-only) properties for test to ensure Consensus is computed
-   * for colour Above PID testing
+   * configure (read-only) properties for test to ensure Consensus is computed for
+   * colour Above PID testing
    */
   @BeforeMethod(alwaysRun = true)
   public void setUp()
@@ -161,6 +108,95 @@ public class AlignFrameTest
     }
   }
 
+  public static void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  @Test(groups = "Functional")
+  public void testHideFeatureColumns()
+  {
+    SequenceI seq1 = new Sequence("Seq1", "ABCDEFGHIJ");
+    SequenceI seq2 = new Sequence("Seq2", "ABCDEFGHIJ");
+    seq1.addSequenceFeature(new SequenceFeature("Metal", "", 1, 5, 0f, null));
+    seq2.addSequenceFeature(new SequenceFeature("Metal", "", 6, 10, 10f,
+            null));
+    seq1.addSequenceFeature(new SequenceFeature("Turn", "", 2, 4,
+            Float.NaN, null));
+    seq2.addSequenceFeature(new SequenceFeature("Turn", "", 7, 9,
+            Float.NaN, null));
+    AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
+    AlignFrame alignFrame = new AlignFrame(al, al.getWidth(),
+            al.getHeight());
+
+    /*
+     * make all features visible (select feature columns checks visibility)
+     */
+    alignFrame.getFeatureRenderer().findAllFeatures(true);
+
+    /*
+     * hiding a feature not present does nothing
+     */
+    assertFalse(alignFrame.hideFeatureColumns("exon", true));
+    assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
+
+    assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
+            .getNumberOfRegions(), 0);
+
+    assertFalse(alignFrame.hideFeatureColumns("exon", false));
+    assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
+
+    assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
+            .getNumberOfRegions(), 0);
+
+    /*
+     * hiding a feature in all columns does nothing
+     */
+    assertFalse(alignFrame.hideFeatureColumns("Metal", true));
+    assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
+
+    assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
+            .getNumberOfRegions(), 0);
+
+
+    /*
+     * threshold Metal to hide features where score < 5
+     * seq1 feature in columns 1-5 is hidden
+     * seq2 feature in columns 6-10 is shown
+     */
+    FeatureColourI fc = new FeatureColour(null, Color.red, Color.blue, null,
+            0f, 10f);
+    fc.setAboveThreshold(true);
+    fc.setThreshold(5f);
+    alignFrame.getFeatureRenderer().setColour("Metal", fc);
+    assertTrue(alignFrame.hideFeatureColumns("Metal", true));
+    HiddenColumns hidden = alignFrame.getViewport().getAlignment().getHiddenColumns();
+    assertEquals(hidden.getNumberOfRegions(), 1);
+    Iterator<int[]> regions = hidden.iterator();
+    int[] next = regions.next();
+    assertEquals(next[0], 5);
+    assertEquals(next[1], 9);
+
+    /*
+     * hide a feature present in some columns
+     * sequence positions [2-4], [7-9] are column positions
+     * [1-3], [6-8] base zero
+     */
+    alignFrame.getViewport().showAllHiddenColumns();
+    assertTrue(alignFrame.hideFeatureColumns("Turn", true));
+    regions = alignFrame.getViewport().getAlignment()
+            .getHiddenColumns().iterator();
+    assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
+            .getNumberOfRegions(), 2);
+    next = regions.next();
+    assertEquals(next[0], 1);
+    assertEquals(next[1], 3);
+    next = regions.next();
+    assertEquals(next[0], 6);
+    assertEquals(next[1], 8);
+  }
+
   /**
    * Test that changing background (alignment) colour scheme
    * <ul>
@@ -540,10 +576,11 @@ public class AlignFrameTest
     assertEquals(af.alignPanel.getViewName(), "View 1");
     AlignViewport av2 = af.getViewport();
     assertNotSame(av, av2);
+    assertSame(av2, af.alignPanel.av);
     rs = av2.getResidueShading();
     assertNotSame(av.getResidueShading(), rs);
     assertEquals(rs.getThreshold(), 10);
-    assertTrue(rs.conservationApplied());
+    assertTrue(rs.conservationApplied(), rs.toString());
     assertEquals(rs.getConservationInc(), 20);
     assertEquals(av2.getAlignment().getGroups().size(), 1);
     sg = av2.getAlignment().getGroups().get(0);
@@ -564,4 +601,26 @@ public class AlignFrameTest
     sp.valueChanged(22);
     assertEquals(av2.getResidueShading().getConservationInc(), 22);
   }
+
+  /**
+   * Verify that making a New View preserves the dataset reference for the
+   * alignment. Otherwise, see a 'duplicate jar entry' reference when trying to
+   * save alignments with multiple views, and codon mappings will not be shared
+   * across all panels in a split frame.
+   * 
+   * @see Jalview2xmlTests#testStoreAndRecoverColourThresholds()
+   */
+  @Test(groups = "Functional")
+  public void testNewView_dsRefPreserved()
+  {
+    AlignViewport av = af.getViewport();
+    AlignmentI al = av.getAlignment();
+    AlignmentI original_ds = al.getDataset();
+    af.newView_actionPerformed(null);
+    assertNotEquals("New view didn't select the a new panel", av,
+            af.getViewport());
+    org.testng.Assert.assertEquals(original_ds,
+            af.getViewport().getAlignment().getDataset(),
+            "Dataset was not preserved in new view");
+  }
 }