JAL-2593 avoid redundant rendering of co-located features

[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 31348c6..3e27aba 100644 (file)
--- a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
+++ b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
@@ -14,6 +14,7 @@ import jalview.io.FileLoader;
 import jalview.schemes.FeatureColour;
 
 import java.awt.Color;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 import java.util.Map;
@@ -252,4 +253,105 @@ public class FeatureRendererTest
     assertEquals(features.size(), 1);
     assertTrue(features.contains(sf8));
   }
+
+  @Test(groups = "Functional")
+  public void testFilterFeaturesForDisplay()
+  {
+    String seqData = ">s1\nabcdef\n";
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
+            DataSourceType.PASTE);
+    AlignViewportI av = af.getViewport();
+    FeatureRenderer fr = new FeatureRenderer(av);
+
+    List<SequenceFeature> features = new ArrayList<>();
+    fr.filterFeaturesForDisplay(features, null); // empty list, does nothing
+
+    SequenceI seq = av.getAlignment().getSequenceAt(0);
+    SequenceFeature sf1 = new SequenceFeature("Cath", "", 6, 8, "group1");
+    seq.addSequenceFeature(sf1);
+    SequenceFeature sf2 = new SequenceFeature("Cath", "", 5, 11, "group2");
+    seq.addSequenceFeature(sf2);
+    SequenceFeature sf3 = new SequenceFeature("Cath", "", 5, 11, "group3");
+    seq.addSequenceFeature(sf3);
+    SequenceFeature sf4 = new SequenceFeature("Cath", "", 6, 8, "group4");
+    seq.addSequenceFeature(sf4);
+    SequenceFeature sf5 = new SequenceFeature("Cath", "", 6, 9, "group4");
+    seq.addSequenceFeature(sf5);
+
+    fr.findAllFeatures(true);
+
+    features = seq.getSequenceFeatures();
+    assertEquals(features.size(), 5);
+    assertTrue(features.contains(sf1));
+    assertTrue(features.contains(sf2));
+    assertTrue(features.contains(sf3));
+    assertTrue(features.contains(sf4));
+    assertTrue(features.contains(sf5));
+
+    /*
+     * filter out duplicate (co-located) features
+     * note: which gets removed is not guaranteed
+     */
+    fr.filterFeaturesForDisplay(features, new FeatureColour(Color.blue));
+    assertEquals(features.size(), 3);
+    assertTrue(features.contains(sf1) || features.contains(sf4));
+    assertFalse(features.contains(sf1) && features.contains(sf4));
+    assertTrue(features.contains(sf2) || features.contains(sf3));
+    assertFalse(features.contains(sf2) && features.contains(sf3));
+    assertTrue(features.contains(sf5));
+
+    /*
+     * hide group 3 - sf3 is removed, sf2 is retained
+     */
+    fr.setGroupVisibility("group3", false);
+    features = seq.getSequenceFeatures();
+    fr.filterFeaturesForDisplay(features, new FeatureColour(Color.blue));
+    assertEquals(features.size(), 3);
+    assertTrue(features.contains(sf1) || features.contains(sf4));
+    assertFalse(features.contains(sf1) && features.contains(sf4));
+    assertTrue(features.contains(sf2));
+    assertFalse(features.contains(sf3));
+    assertTrue(features.contains(sf5));
+
+    /*
+     * hide group 2, show group 3 - sf2 is removed, sf3 is retained
+     */
+    fr.setGroupVisibility("group2", false);
+    fr.setGroupVisibility("group3", true);
+    features = seq.getSequenceFeatures();
+    fr.filterFeaturesForDisplay(features, null);
+    assertEquals(features.size(), 3);
+    assertTrue(features.contains(sf1) || features.contains(sf4));
+    assertFalse(features.contains(sf1) && features.contains(sf4));
+    assertFalse(features.contains(sf2));
+    assertTrue(features.contains(sf3));
+    assertTrue(features.contains(sf5));
+
+    /*
+     * no filtering of co-located features with graduated colour scheme
+     * sf2 is removed as its group is hidden
+     */
+    features = seq.getSequenceFeatures();
+    fr.filterFeaturesForDisplay(features, new FeatureColour(Color.black,
+            Color.white, 0f, 1f));
+    assertEquals(features.size(), 4);
+    assertTrue(features.contains(sf1));
+    assertTrue(features.contains(sf3));
+    assertTrue(features.contains(sf4));
+    assertTrue(features.contains(sf5));
+
+    /*
+     * filtering of co-located features with colour by label
+     */
+    features = seq.getSequenceFeatures();
+    FeatureColour fc = new FeatureColour(Color.black);
+    fc.setColourByLabel(true);
+    fr.filterFeaturesForDisplay(features, fc);
+    assertEquals(features.size(), 3);
+    assertTrue(features.contains(sf1) || features.contains(sf4));
+    assertFalse(features.contains(sf1) && features.contains(sf4));
+    assertFalse(features.contains(sf2));
+    assertTrue(features.contains(sf3));
+    assertTrue(features.contains(sf5));
+  }
 }