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"));
}