import jalview.datamodel.SequenceI;
import jalview.gui.AlignViewport;
import jalview.gui.JvOptionPane;
-import jalview.gui.Preferences;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.UserColourScheme;
import jalview.schemes.ZappoColourScheme;
final AlignViewport av = new AlignViewport(al);
ResidueColourFinder rcf = new OverviewResColourFinder();
+ ResidueShaderI sh = av.getResidueShading();
+
// gaps are grey, residues white
- assertEquals(Color.white, rcf.getResidueColour(true,
- av.getResidueShading(),
- null, seq, 0, null));
- assertEquals(Color.lightGray, rcf
- .getResidueColour(true, av.getResidueShading(), null, seq, 2,
- null));
+ assertEquals(Color.white,
+ rcf.getResidueColour(true, sh, null, seq, 0, null));
+ System.out.println(rcf.getResidueColour(true, sh, null, seq, 2, null));
+ assertEquals(Color.lightGray, rcf.getResidueColour(true,
+ sh, null, seq, 2, null));
// unaffected by showBoxes setting
assertEquals(Color.white, rcf.getResidueColour(false,
- av.getResidueShading(), null, seq, 0, null));
+ sh, null, seq, 0, null));
assertEquals(Color.lightGray, rcf.getResidueColour(false,
- av.getResidueShading(), null, seq, 2, null));
+ sh, null, seq, 2, null));
}
@Test(groups = { "Functional" })
// unaffected by showBoxes setting
// gap colour not specified so gaps are lightGray
newColours[23] = null;
+
assertEquals(Color.lightGray, rcf.getResidueColour(false,
av.getResidueShading(), null, seq, 3, null));
av.getResidueShading(), null, seq, 3, null));
}
- @Test
+ @Test(groups = "Functional")
public void testGetResidueBoxColour_group()
{
SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
assertEquals(Color.lightGray, rcf.getResidueColour(false,
av.getResidueShading(), groups, seq, 2, null));
+ // use legacy colouring
rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
// G in group specified as magenta in Zappo
// Gap outside group coloured white
assertEquals(Color.white, rcf.getResidueColour(false,
av.getResidueShading(), groups, seq, 2, null));
+
+ // use new colouring
+ rcf = new OverviewResColourFinder(false, Color.blue, 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
+ @Test(groups = "Functional")
public void testGetBoxColour()
{
SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
// gaps gap colour
c = rcf.getBoxColour(shader, seq, 3);
- assertEquals(Preferences.OVERVIEW_DEFAULT_GAP, c);
+ assertEquals(
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP,
+ c);
// legacy colouring set explicitly via constructor
rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
// gaps gap colour
c = rcf.getBoxColour(shader, seq, 3);
- assertEquals(Preferences.OVERVIEW_DEFAULT_GAP, c);
+ assertEquals(
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP,
+ c);
// non legacy colouring with colour scheme
rcf = new OverviewResColourFinder(false, Color.blue, Color.red);