JAL-2483 JAL-2481 fixed findAllFeatures to handle null group correctly

[jalview.git] / test / jalview / renderer / seqfeatures / FeatureRendererTest.java

diff --git a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
index febd306..ab5c137 100644 (file)
--- a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
+++ b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
@@ -63,16 +63,21 @@ public class FeatureRendererTest
     seqs.get(2).addSequenceFeature(
             new SequenceFeature("Rfam", "Desc", 5, 9, Float.NaN,
                     "RfamGroup"));
+    // existing feature type with null group
     seqs.get(3).addSequenceFeature(
             new SequenceFeature("Rfam", "Desc", 5, 9, Float.NaN, null));
+    // new feature type with null group
+    seqs.get(3).addSequenceFeature(
+            new SequenceFeature("Scop", "Desc", 5, 9, Float.NaN, null));
     // null value for type produces NullPointerException
     fr.findAllFeatures(true);
     types = fr.getRenderOrder();
     groups = fr.getFeatureGroups();
-    assertEquals(types.size(), 2);
+    assertEquals(types.size(), 3);
     assertFalse(types.contains("Type"));
     assertTrue(types.contains("Pfam"));
     assertTrue(types.contains("Rfam"));
+    assertTrue(types.contains("Scop"));
     assertEquals(groups.size(), 2);
     assertFalse(groups.contains("Group"));
     assertTrue(groups.contains("PfamGroup"));
@@ -104,18 +109,19 @@ public class FeatureRendererTest
      * check render order (last is on top)
      */
     List<String> renderOrder = fr.getRenderOrder();
-    assertEquals(renderOrder, Arrays.asList("Rfam", "Pfam"));
+    assertEquals(renderOrder, Arrays.asList("Scop", "Rfam", "Pfam"));
 
     /*
      * change render order (todo: an easier way)
      * nb here last comes first in the data array
      */
-    Object[][] data = new Object[2][];
+    Object[][] data = new Object[3][];
     FeatureColourI colour = new FeatureColour(Color.RED);
     data[0] = new Object[] { "Rfam", colour, true };
     data[1] = new Object[] { "Pfam", colour, false };
+    data[2] = new Object[] { "Scop", colour, false };
     fr.setFeaturePriority(data);
-    assertEquals(fr.getRenderOrder(), Arrays.asList("Pfam", "Rfam"));
+    assertEquals(fr.getRenderOrder(), Arrays.asList("Scop", "Pfam", "Rfam"));
     assertEquals(fr.getDisplayedFeatureTypes(), Arrays.asList("Rfam"));
 
     /*
@@ -126,8 +132,104 @@ public class FeatureRendererTest
             new SequenceFeature("Metal", "Desc", 14, 22, 8f, "MetalGroup"));
     fr.findAllFeatures(true);
     assertEquals(fr.getRenderOrder(),
-            Arrays.asList("Pfam", "Rfam", "Metal"));
+            Arrays.asList("Scop", "Pfam", "Rfam", "Metal"));
     assertEquals(fr.getDisplayedFeatureTypes(),
             Arrays.asList("Rfam", "Metal"));
   }
+
+  @Test(groups = "Functional")
+  public void testFindFeaturesAtRes()
+  {
+    String seqData = ">s1\nabcdefghijklmnopqrstuvwxyz\n";
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
+            DataSourceType.PASTE);
+    AlignViewportI av = af.getViewport();
+    FeatureRenderer fr = new FeatureRenderer(av);
+    SequenceI seq = av.getAlignment().getSequenceAt(0);
+
+    /*
+     * with no features
+     */
+    List<SequenceFeature> features = fr.findFeaturesAtRes(seq, 3);
+    assertTrue(features.isEmpty());
+
+    /*
+     * add features
+     */
+    SequenceFeature sf1 = new SequenceFeature("Type1", "Desc", 0, 0, 1f,
+            "Group"); // non-positional
+    seq.addSequenceFeature(sf1);
+    SequenceFeature sf2 = new SequenceFeature("Type2", "Desc", 5, 15, 1f,
+            "Group1");
+    seq.addSequenceFeature(sf2);
+    SequenceFeature sf3 = new SequenceFeature("Type3", "Desc", 5, 15, 1f,
+            "Group2");
+    seq.addSequenceFeature(sf3);
+    SequenceFeature sf4 = new SequenceFeature("Type3", "Desc", 5, 15, 1f,
+            null); // null group is always treated as visible
+    seq.addSequenceFeature(sf4);
+
+    /*
+     * add contact features
+     */
+    SequenceFeature sf5 = new SequenceFeature("Disulphide Bond", "Desc", 4,
+            12, 1f, "Group1");
+    seq.addSequenceFeature(sf5);
+    SequenceFeature sf6 = new SequenceFeature("Disulphide Bond", "Desc", 4,
+            12, 1f, "Group2");
+    seq.addSequenceFeature(sf6);
+    SequenceFeature sf7 = new SequenceFeature("Disulphide Bond", "Desc", 4,
+            12, 1f, null);
+    seq.addSequenceFeature(sf7);
+
+    /*
+     * let feature renderer discover features (and make visible)
+     */
+    fr.findAllFeatures(true);
+    features = fr.findFeaturesAtRes(seq, 12); // all positional
+    assertEquals(features.size(), 6);
+    assertTrue(features.contains(sf2));
+    assertTrue(features.contains(sf3));
+    assertTrue(features.contains(sf4));
+    assertTrue(features.contains(sf5));
+    assertTrue(features.contains(sf6));
+    assertTrue(features.contains(sf7));
+
+    /*
+     * at a non-contact position
+     */
+    features = fr.findFeaturesAtRes(seq, 11);
+    assertEquals(features.size(), 3);
+    assertTrue(features.contains(sf2));
+    assertTrue(features.contains(sf3));
+    assertTrue(features.contains(sf4));
+
+    /*
+     * make "Type2" not displayed
+     */
+    Object[][] data = new Object[4][];
+    FeatureColourI colour = new FeatureColour(Color.RED);
+    data[0] = new Object[] { "Type1", colour, true };
+    data[1] = new Object[] { "Type2", colour, false };
+    data[2] = new Object[] { "Type3", colour, true };
+    data[3] = new Object[] { "Disulphide Bond", colour, true };
+    fr.setFeaturePriority(data);
+    features = fr.findFeaturesAtRes(seq, 12);
+    assertEquals(features.size(), 5); // no sf2
+    assertTrue(features.contains(sf3));
+    assertTrue(features.contains(sf4));
+    assertTrue(features.contains(sf5));
+    assertTrue(features.contains(sf6));
+    assertTrue(features.contains(sf7));
+
+    /*
+     * make "Group2" not displayed
+     */
+    fr.setGroupVisibility("Group2", false);
+    features = fr.findFeaturesAtRes(seq, 12);
+    assertEquals(features.size(), 3); // no sf2, sf3, sf6
+    assertTrue(features.contains(sf4));
+    assertTrue(features.contains(sf5));
+    assertTrue(features.contains(sf7));
+  }
 }