X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignFrameTest.java;h=b0aaab9ec03a0651dc12b8e6e7f539e303c5817f;hb=356260e6aa37640091849355ed97cd4103cc4c6c;hp=1d8b2404a82e7cffd250a6b912235edba33180e3;hpb=613818a08b858e3fe0dd778c738a362b3a4a0882;p=jalview.git

diff --git a/test/jalview/gui/AlignFrameTest.java b/test/jalview/gui/AlignFrameTest.java
index 1d8b240..b0aaab9 100644
--- a/test/jalview/gui/AlignFrameTest.java
+++ b/test/jalview/gui/AlignFrameTest.java
@@ -26,11 +26,12 @@ import static org.testng.Assert.assertNotSame;
 import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 
-import jalview.api.AlignCalcManagerI;
+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;
@@ -40,6 +41,7 @@ import jalview.io.FileLoader;
 import jalview.io.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;
@@ -47,7 +49,7 @@ 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;
@@ -70,54 +72,81 @@ public class AlignFrameTest
   {
     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("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());
+    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());
-    assertTrue(alignFrame.getViewport().getAlignment().getHiddenColumns()
-            .getHiddenColumnsCopy()
-            .isEmpty());
+
+    assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
+            .getNumberOfRegions(), 0);
+
     assertFalse(alignFrame.hideFeatureColumns("exon", false));
     assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
-    assertTrue(alignFrame.getViewport().getAlignment().getHiddenColumns()
-            .getHiddenColumnsCopy()
-            .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());
-    List<int[]> hidden = alignFrame.getViewport().getAlignment()
-            .getHiddenColumns()
-            .getHiddenColumnsCopy();
-    assertTrue(hidden.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(Color.red, Color.blue, 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));
-    hidden = alignFrame.getViewport().getAlignment().getHiddenColumns()
-            .getHiddenColumnsCopy();
-    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);
+    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);
   }
 
   @BeforeClass(alwaysRun = true)
@@ -539,24 +568,13 @@ public class AlignFrameTest
             new String[] { "Background" }));
 
     /*
-     * make a new View, wait for Conservation thread to complete,
-     * verify alignment and group colour schemes
+     * make a new View, verify alignment and group colour schemes
      */
     af.newView_actionPerformed(null);
     assertEquals(af.alignPanel.getViewName(), "View 1");
     AlignViewport av2 = af.getViewport();
     assertNotSame(av, av2);
     assertSame(av2, af.alignPanel.av);
-    AlignCalcManagerI calcManager = av2.getCalcManager();
-    do
-    {
-      try
-      {
-        Thread.sleep(50);
-      } catch (InterruptedException x)
-      {
-      }
-    } while (calcManager.isWorking());
     rs = av2.getResidueShading();
     assertNotSame(av.getResidueShading(), rs);
     assertEquals(rs.getThreshold(), 10);