import jalview.schemes.FeatureColour;
import java.awt.Color;
+import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
seqs.get(2).addSequenceFeature(
new SequenceFeature("Rfam", "Desc", 5, 9, Float.NaN,
"RfamGroup"));
+ // existing feature type with null group
seqs.get(3).addSequenceFeature(
new SequenceFeature("Rfam", "Desc", 5, 9, Float.NaN, null));
+ // new feature type with null group
+ seqs.get(3).addSequenceFeature(
+ new SequenceFeature("Scop", "Desc", 5, 9, Float.NaN, null));
// null value for type produces NullPointerException
fr.findAllFeatures(true);
types = fr.getRenderOrder();
groups = fr.getFeatureGroups();
- assertEquals(types.size(), 2);
+ assertEquals(types.size(), 3);
assertFalse(types.contains("Type"));
assertTrue(types.contains("Pfam"));
assertTrue(types.contains("Rfam"));
+ assertTrue(types.contains("Scop"));
assertEquals(groups.size(), 2);
assertFalse(groups.contains("Group"));
assertTrue(groups.contains("PfamGroup"));
* check render order (last is on top)
*/
List<String> renderOrder = fr.getRenderOrder();
- assertEquals(renderOrder, Arrays.asList("Rfam", "Pfam"));
+ assertEquals(renderOrder, Arrays.asList("Scop", "Rfam", "Pfam"));
/*
* change render order (todo: an easier way)
* nb here last comes first in the data array
*/
- Object[][] data = new Object[2][];
+ Object[][] data = new Object[3][];
FeatureColourI colour = new FeatureColour(Color.RED);
data[0] = new Object[] { "Rfam", colour, true };
data[1] = new Object[] { "Pfam", colour, false };
+ data[2] = new Object[] { "Scop", colour, false };
fr.setFeaturePriority(data);
- assertEquals(fr.getRenderOrder(), Arrays.asList("Pfam", "Rfam"));
+ assertEquals(fr.getRenderOrder(), Arrays.asList("Scop", "Pfam", "Rfam"));
assertEquals(fr.getDisplayedFeatureTypes(), Arrays.asList("Rfam"));
/*
new SequenceFeature("Metal", "Desc", 14, 22, 8f, "MetalGroup"));
fr.findAllFeatures(true);
assertEquals(fr.getRenderOrder(),
- Arrays.asList("Pfam", "Rfam", "Metal"));
+ Arrays.asList("Scop", "Pfam", "Rfam", "Metal"));
assertEquals(fr.getDisplayedFeatureTypes(),
Arrays.asList("Rfam", "Metal"));
}
@Test(groups = "Functional")
- public void testFindFeaturesAtRes()
+ public void testFindFeaturesAtColumn()
{
- String seqData = ">s1\nabcdefghijklmnopqrstuvwxyz\n";
+ String seqData = ">s1/4-29\n-ab--cdefghijklmnopqrstuvwxyz\n";
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
DataSourceType.PASTE);
AlignViewportI av = af.getViewport();
/*
* with no features
*/
- List<SequenceFeature> features = fr.findFeaturesAtRes(seq, 3);
+ List<SequenceFeature> features = fr.findFeaturesAtColumn(seq, 3);
assertTrue(features.isEmpty());
/*
SequenceFeature sf1 = new SequenceFeature("Type1", "Desc", 0, 0, 1f,
"Group"); // non-positional
seq.addSequenceFeature(sf1);
- SequenceFeature sf2 = new SequenceFeature("Type2", "Desc", 5, 15, 1f,
+ SequenceFeature sf2 = new SequenceFeature("Type2", "Desc", 8, 18, 1f,
"Group1");
seq.addSequenceFeature(sf2);
- SequenceFeature sf3 = new SequenceFeature("Type3", "Desc", 5, 15, 1f,
+ SequenceFeature sf3 = new SequenceFeature("Type3", "Desc", 8, 18, 1f,
"Group2");
seq.addSequenceFeature(sf3);
- SequenceFeature sf4 = new SequenceFeature("Type3", "Desc", 5, 15, 1f,
+ SequenceFeature sf4 = new SequenceFeature("Type3", "Desc", 8, 18, 1f,
null); // null group is always treated as visible
seq.addSequenceFeature(sf4);
/*
* add contact features
*/
- SequenceFeature sf5 = new SequenceFeature("Disulphide Bond", "Desc", 4,
- 12, 1f, "Group1");
+ SequenceFeature sf5 = new SequenceFeature("Disulphide Bond", "Desc", 7,
+ 15, 1f, "Group1");
seq.addSequenceFeature(sf5);
- SequenceFeature sf6 = new SequenceFeature("Disulphide Bond", "Desc", 4,
- 12, 1f, "Group2");
+ SequenceFeature sf6 = new SequenceFeature("Disulphide Bond", "Desc", 7,
+ 15, 1f, "Group2");
seq.addSequenceFeature(sf6);
- SequenceFeature sf7 = new SequenceFeature("Disulphide Bond", "Desc", 4,
- 12, 1f, null);
+ SequenceFeature sf7 = new SequenceFeature("Disulphide Bond", "Desc", 7,
+ 15, 1f, null);
seq.addSequenceFeature(sf7);
+ // feature spanning B--C
+ SequenceFeature sf8 = new SequenceFeature("Type1", "Desc", 5, 6, 1f,
+ "Group");
+ seq.addSequenceFeature(sf8);
+ // contact feature B/C
+ SequenceFeature sf9 = new SequenceFeature("Disulphide Bond", "Desc", 5,
+ 6, 1f, "Group");
+ seq.addSequenceFeature(sf9);
+
/*
* let feature renderer discover features (and make visible)
*/
fr.findAllFeatures(true);
- features = fr.findFeaturesAtRes(seq, 12); // all positional
+ features = fr.findFeaturesAtColumn(seq, 15); // all positional
assertEquals(features.size(), 6);
assertTrue(features.contains(sf2));
assertTrue(features.contains(sf3));
/*
* at a non-contact position
*/
- features = fr.findFeaturesAtRes(seq, 11);
+ features = fr.findFeaturesAtColumn(seq, 14);
assertEquals(features.size(), 3);
assertTrue(features.contains(sf2));
assertTrue(features.contains(sf3));
data[2] = new Object[] { "Type3", colour, true };
data[3] = new Object[] { "Disulphide Bond", colour, true };
fr.setFeaturePriority(data);
- features = fr.findFeaturesAtRes(seq, 12);
+
+ features = fr.findFeaturesAtColumn(seq, 15);
assertEquals(features.size(), 5); // no sf2
assertTrue(features.contains(sf3));
assertTrue(features.contains(sf4));
* make "Group2" not displayed
*/
fr.setGroupVisibility("Group2", false);
- features = fr.findFeaturesAtRes(seq, 12);
+
+ features = fr.findFeaturesAtColumn(seq, 15);
assertEquals(features.size(), 3); // no sf2, sf3, sf6
assertTrue(features.contains(sf4));
assertTrue(features.contains(sf5));
assertTrue(features.contains(sf7));
+
+ // features 'at' a gap between b and c
+ // - returns enclosing feature BC but not contact feature B/C
+ features = fr.findFeaturesAtColumn(seq, 4);
+ assertEquals(features.size(), 1);
+ assertTrue(features.contains(sf8));
+ features = fr.findFeaturesAtColumn(seq, 5);
+ 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, 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, 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
+ * 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));
+
+ /*
+ * co-located features with colour by label
+ * should not get filtered
+ */
+ features = seq.getSequenceFeatures();
+ FeatureColour fc = new FeatureColour(Color.black);
+ fc.setColourByLabel(true);
+ fr.filterFeaturesForDisplay(features, fc);
+ assertEquals(features.size(), 4);
+ assertTrue(features.contains(sf1));
+ assertTrue(features.contains(sf3));
+ assertTrue(features.contains(sf4));
+ assertTrue(features.contains(sf5));
}
}
git://source.jalview.org / jalview.git / blobdiff