JAL-2816 tweaks to feature visibility checks

[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..438feba 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 +253,70 @@ 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); // empty list, does nothing
+
+    SequenceI seq = av.getAlignment().getSequenceAt(0);
+    SequenceFeature sf1 = new SequenceFeature("Cath", "", 6, 8, Float.NaN,
+            "group1");
+    seq.addSequenceFeature(sf1);
+    SequenceFeature sf2 = new SequenceFeature("Cath", "", 5, 11, 2f,
+            "group2");
+    seq.addSequenceFeature(sf2);
+    SequenceFeature sf3 = new SequenceFeature("Cath", "", 5, 11, 3f,
+            "group3");
+    seq.addSequenceFeature(sf3);
+    SequenceFeature sf4 = new SequenceFeature("Cath", "", 6, 8, 4f,
+            "group4");
+    seq.addSequenceFeature(sf4);
+    SequenceFeature sf5 = new SequenceFeature("Cath", "", 6, 9, 5f,
+            "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);
+    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 groups 2 and 3 makes no difference to this method
+     */
+    fr.setGroupVisibility("group2", false);
+    fr.setGroupVisibility("group3", false);
+    features = seq.getSequenceFeatures();
+    fr.filterFeaturesForDisplay(features);
+    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));
+  }
 }