import static org.testng.AssertJUnit.assertEquals;
+import java.awt.Color;
+import java.util.ArrayList;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignViewport;
import jalview.gui.JvOptionPane;
-import jalview.gui.Preferences;
+import jalview.gui.OverviewCanvas;
+import jalview.schemes.ColourSchemeI;
import jalview.schemes.UserColourScheme;
import jalview.schemes.ZappoColourScheme;
-import java.awt.Color;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
public class OverviewResColourFinderTest
{
{
JvOptionPane.setInteractiveMode(false);
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
}
@Test(groups = { "Functional" })
// 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));
+ av.getResidueShading(), null, seq, 0, null));
+ assertEquals(Color.lightGray, rcf.getResidueColour(true,
+ av.getResidueShading(), null, seq, 2, null));
// unaffected by showBoxes setting
assertEquals(Color.white, rcf.getResidueColour(false,
av.setGlobalColourScheme(new ZappoColourScheme());
// @see ResidueProperties.zappo
- assertEquals(Color.pink,
- rcf.getResidueColour(true, av.getResidueShading(),
- null, seq, 0, null)); // M
- assertEquals(Color.green,
- rcf.getResidueColour(true, av.getResidueShading(),
- null, seq, 2, null)); // T
- assertEquals(Color.magenta,
- rcf.getResidueColour(true, av.getResidueShading(),
- null, seq, 5, null)); // G
- assertEquals(Color.orange,
- rcf.getResidueColour(true, av.getResidueShading(),
- null, seq, 12, null)); // F
+ assertEquals(Color.pink, rcf.getResidueColour(true,
+ av.getResidueShading(), null, seq, 0, null)); // M
+ assertEquals(Color.green, rcf.getResidueColour(true,
+ av.getResidueShading(), null, seq, 2, null)); // T
+ assertEquals(Color.magenta, rcf.getResidueColour(true,
+ av.getResidueShading(), null, seq, 5, null)); // G
+ assertEquals(Color.orange, rcf.getResidueColour(true,
+ av.getResidueShading(), null, seq, 12, null)); // F
// gap colour not specified so gaps are lightGray
- assertEquals(Color.lightGray, rcf
- .getResidueColour(true, av.getResidueShading(), null, seq, 3,
- null));
+ assertEquals(Color.lightGray, rcf.getResidueColour(true,
+ av.getResidueShading(), null, seq, 3, null));
// unaffected by showBoxes setting
assertEquals(Color.pink, rcf.getResidueColour(false,
av.getResidueShading(), null, seq, 12, null)); // F
// gap colour not specified so gaps are lightGray
- assertEquals(Color.lightGray, rcf
- .getResidueColour(false, av.getResidueShading(), null, seq, 3,
- null));
+ assertEquals(Color.lightGray, rcf.getResidueColour(false,
+ av.getResidueShading(), null, seq, 3, null));
}
av.setGlobalColourScheme(new UserColourScheme(newColours));
// gap colour not specified so gaps are lightGray
- assertEquals(Color.lightGray, rcf
- .getResidueColour(true, av.getResidueShading(), null, seq, 3,
- null));
+ assertEquals(Color.lightGray, rcf.getResidueColour(true,
+ av.getResidueShading(), null, seq, 3, null));
newColours[23] = Color.pink;
av.setGlobalColourScheme(new UserColourScheme(newColours));
// gap colour specified as pink
assertEquals(Color.pink, rcf.getResidueColour(true,
- av.getResidueShading(),
- null, seq, 3, null));
+ av.getResidueShading(), null, seq, 3, null));
// unaffected by showBoxes setting
// gap colour not specified so gaps are lightGray
}
@Test
- public void testGetBoxColour()
+ public void testGetResidueBoxColour_group()
{
- Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
+ AlignmentI al = new Alignment(new SequenceI[] { seq });
+ 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()
+ {
SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
// gap
AlignmentI al = new Alignment(new SequenceI[] { seq });
// gaps gap colour
c = rcf.getBoxColour(shader, seq, 3);
- assertEquals(Preferences.OVERVIEW_DEFAULT_GAP, c);
+ assertEquals(OverviewCanvas.OVERVIEW_DEFAULT_GAP, c);
// legacy colouring set explicitly via constructor
- rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
+ rcf = new OverviewResColourFinder(Color.white, Color.lightGray, Color.red);
shader = new ResidueShader();
// residues light gray
// gaps gap colour
c = rcf.getBoxColour(shader, seq, 3);
- assertEquals(Preferences.OVERVIEW_DEFAULT_GAP, c);
+ assertEquals(OverviewCanvas.OVERVIEW_DEFAULT_GAP, c);
// non legacy colouring with colour scheme
- rcf = new OverviewResColourFinder(false, Color.blue, Color.red);
+ rcf = new OverviewResColourFinder(Color.blue, Color.white, Color.red);
shader = new ResidueShader(new ZappoColourScheme());
// M residue pink
assertEquals(Color.blue, c);
// legacy colouring with colour scheme
- rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
+ rcf = new OverviewResColourFinder(Color.white, Color.lightGray, Color.red);
// M residue pink
c = rcf.getBoxColour(shader, seq, 0);