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 3e27aba..438feba 100644 (file)
--- a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
+++ b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
@@ -264,18 +264,23 @@ public class FeatureRendererTest
     FeatureRenderer fr = new FeatureRenderer(av);
 
     List<SequenceFeature> features = new ArrayList<>();
-    fr.filterFeaturesForDisplay(features, null); // empty list, does nothing
+    fr.filterFeaturesForDisplay(features); // empty list, does nothing
 
     SequenceI seq = av.getAlignment().getSequenceAt(0);
-    SequenceFeature sf1 = new SequenceFeature("Cath", "", 6, 8, "group1");
+    SequenceFeature sf1 = new SequenceFeature("Cath", "", 6, 8, Float.NaN,
+            "group1");
     seq.addSequenceFeature(sf1);
-    SequenceFeature sf2 = new SequenceFeature("Cath", "", 5, 11, "group2");
+    SequenceFeature sf2 = new SequenceFeature("Cath", "", 5, 11, 2f,
+            "group2");
     seq.addSequenceFeature(sf2);
-    SequenceFeature sf3 = new SequenceFeature("Cath", "", 5, 11, "group3");
+    SequenceFeature sf3 = new SequenceFeature("Cath", "", 5, 11, 3f,
+            "group3");
     seq.addSequenceFeature(sf3);
-    SequenceFeature sf4 = new SequenceFeature("Cath", "", 6, 8, "group4");
+    SequenceFeature sf4 = new SequenceFeature("Cath", "", 6, 8, 4f,
+            "group4");
     seq.addSequenceFeature(sf4);
-    SequenceFeature sf5 = new SequenceFeature("Cath", "", 6, 9, "group4");
+    SequenceFeature sf5 = new SequenceFeature("Cath", "", 6, 9, 5f,
+            "group4");
     seq.addSequenceFeature(sf5);
 
     fr.findAllFeatures(true);
@@ -292,7 +297,7 @@ public class FeatureRendererTest
      * filter out duplicate (co-located) features
      * note: which gets removed is not guaranteed
      */
-    fr.filterFeaturesForDisplay(features, new FeatureColour(Color.blue));
+    fr.filterFeaturesForDisplay(features);
     assertEquals(features.size(), 3);
     assertTrue(features.contains(sf1) || features.contains(sf4));
     assertFalse(features.contains(sf1) && features.contains(sf4));
@@ -301,57 +306,17 @@ public class FeatureRendererTest
     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
+     * hide groups 2 and 3 makes no difference to this method
      */
     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
-     */
+    fr.setGroupVisibility("group3", false);
     features = seq.getSequenceFeatures();
-    FeatureColour fc = new FeatureColour(Color.black);
-    fc.setColourByLabel(true);
-    fr.filterFeaturesForDisplay(features, fc);
+    fr.filterFeaturesForDisplay(features);
     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(sf2) || features.contains(sf3));
+    assertFalse(features.contains(sf2) && features.contains(sf3));
     assertTrue(features.contains(sf5));
   }
 }