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, Float.NaN,
* 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));
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
- * filterFeaturesForDisplay does _not_ check colour threshold
- * 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));
}
}