From: gmungoc Date: Tue, 23 Oct 2018 14:31:50 +0000 (+0100) Subject: JAL-3139 check group visibility when removing 'redundant' features X-Git-Tag: Release_2_11_0~17^2~85^2 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ef7d9bed59341ba8a035dc4578cd9c62b655286b;p=jalview.git JAL-3139 check group visibility when removing 'redundant' features --- diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java index 553f813..5db8751 100644 --- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java +++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java @@ -1029,11 +1029,11 @@ public abstract class FeatureRendererModel } /** - * Removes from the list of features any that duplicate the location of a - * feature of the same type. Should be used only for features of the same, - * simple, feature colour (which normally implies the same feature type). Does - * not check visibility settings for feature type or feature group. No - * filtering is done if transparency, or any feature filters, are in force. + * Removes from the list of features any whose group is not shown, or that are + * visible and duplicate the location of a visible feature of the same type. + * Should be used only for features of the same, simple, feature colour (which + * normally implies the same feature type). No filtering is done if + * transparency, or any feature filters, are in force. * * @param features */ @@ -1057,6 +1057,11 @@ public abstract class FeatureRendererModel while (it.hasNext()) { SequenceFeature sf = it.next(); + if (featureGroupNotShown(sf)) + { + it.remove(); + continue; + } /* * a feature is redundant for rendering purposes if it has the @@ -1064,7 +1069,8 @@ public abstract class FeatureRendererModel * (checking type and isContactFeature as a fail-safe here, although * currently they are guaranteed to match in this context) */ - if (lastFeature != null && sf.getBegin() == lastFeature.getBegin() + if (lastFeature != null + && sf.getBegin() == lastFeature.getBegin() && sf.getEnd() == lastFeature.getEnd() && sf.isContactFeature() == lastFeature.isContactFeature() && sf.getType().equals(lastFeature.getType())) diff --git a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java index 11b129e..a9e3754 100644 --- a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java +++ b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java @@ -328,18 +328,18 @@ public class FeatureRendererTest 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(sf1); + seq.addSequenceFeature(sf2); + seq.addSequenceFeature(sf3); + seq.addSequenceFeature(sf4); seq.addSequenceFeature(sf5); fr.findAllFeatures(true); @@ -365,17 +365,17 @@ public class FeatureRendererTest assertTrue(features.contains(sf5)); /* - * hide groups 2 and 3 makes no difference to this method + * features in hidden groups are removed */ fr.setGroupVisibility("group2", false); fr.setGroupVisibility("group3", false); features = seq.getSequenceFeatures(); fr.filterFeaturesForDisplay(features); - assertEquals(features.size(), 3); + assertEquals(features.size(), 2); 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)); + assertFalse(features.contains(sf2)); + assertFalse(features.contains(sf3)); assertTrue(features.contains(sf5)); /*