Merge branch 'releases/Release_2_10_4_Branch' into develop

[jalview.git] / test / jalview / gui / AlignFrameTest.java

diff --git a/test/jalview/gui/AlignFrameTest.java b/test/jalview/gui/AlignFrameTest.java
index dd1a4de..b0aaab9 100644 (file)
--- a/test/jalview/gui/AlignFrameTest.java
+++ b/test/jalview/gui/AlignFrameTest.java
@@ -26,10 +26,12 @@ 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;
@@ -39,6 +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;
@@ -69,26 +72,34 @@ 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());
+
     assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
             .getNumberOfRegions(), 0);
+
     assertFalse(alignFrame.hideFeatureColumns("exon", false));
     assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
+
     assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
             .getNumberOfRegions(), 0);
 
@@ -97,20 +108,40 @@ public class AlignFrameTest
      */
     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(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));
-    Iterator<int[]> regions = alignFrame.getViewport().getAlignment()
+    regions = alignFrame.getViewport().getAlignment()
             .getHiddenColumns().iterator();
     assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
             .getNumberOfRegions(), 2);
-    int[] next = regions.next();
+    next = regions.next();
     assertEquals(next[0], 1);
     assertEquals(next[1], 3);
     next = regions.next();