+ ColourSchemeI cs = new ZappoColourScheme();
+ ArrayList<SequenceI> seqlist = new ArrayList<>();
+ seqlist.add(seq);
+ SequenceGroup sg = new SequenceGroup(seqlist, "testgroup", cs, true,
+ true, true, 5, 9);
+ al.addGroup(sg);
+ SequenceGroup[] groups = new SequenceGroup[1];
+ groups[0] = sg;
+
+ final AlignViewport av = new AlignViewport(al);
+ ResidueColourFinder rcf = new OverviewResColourFinder();
+
+ // G in group specified as magenta in Zappo
+ assertEquals(Color.magenta, rcf.getResidueColour(false,
+ av.getResidueShading(), groups, seq, 7, null));
+
+ // Residue outside group coloured white
+ assertEquals(Color.white, rcf.getResidueColour(false,
+ av.getResidueShading(), groups, seq, 0, null));
+
+ // Gap outside group coloured lightgray
+ assertEquals(Color.lightGray, rcf.getResidueColour(false,
+ av.getResidueShading(), groups, seq, 2, null));
+
+ // use legacy colouring
+ rcf = new OverviewResColourFinder(Color.white, Color.lightGray,
+ Color.red);
+
+ // G in group specified as magenta in Zappo
+ assertEquals(Color.magenta, rcf.getResidueColour(false,
+ av.getResidueShading(), groups, seq, 7, null));
+
+ // Residue outside group coloured lightgray
+ assertEquals(Color.lightGray, rcf.getResidueColour(false,
+ av.getResidueShading(), groups, seq, 0, null));
+
+ // Gap outside group coloured white
+ assertEquals(Color.white, rcf.getResidueColour(false,
+ av.getResidueShading(), groups, seq, 2, null));
+
+ // use new colouring
+ rcf = new OverviewResColourFinder(Color.blue, Color.white, Color.red);
+
+ // G in group specified as magenta in Zappo
+ assertEquals(Color.magenta, rcf.getResidueColour(false,
+ av.getResidueShading(), groups, seq, 7, null));
+
+ // Residue outside group coloured white
+ assertEquals(Color.white, rcf.getResidueColour(false,
+ av.getResidueShading(), groups, seq, 0, null));
+
+ // Gap outside group coloured blue
+ assertEquals(Color.blue, rcf.getResidueColour(false,
+ av.getResidueShading(), groups, seq, 2, null));
+ }
+
+ @Test
+ public void testGetBoxColour()
+ {