JAL-2490 findFeaturesAtRes with performant feature lookup

[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..5bda316 100644 (file)
--- a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
+++ b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
@@ -130,4 +130,100 @@ public class FeatureRendererTest
     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));
+  }
 }