import static org.testng.AssertJUnit.assertEquals;
+import jalview.api.AlignViewportI;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.gui.JvOptionPane;
import jalview.schemes.UserColourScheme;
import jalview.schemes.ZappoColourScheme;
-
import java.awt.Color;
import org.testng.annotations.BeforeClass;
{
SequenceI seq = new Sequence("name", "MATVLGSPRAPAFF"); // FER1_MAIZE...
AlignmentI al = new Alignment(new SequenceI[] { seq });
- final AlignViewport av = new AlignViewport(al);
+ final AlignViewportI av = new AlignViewport(al);
ResidueColourFinder rcf = new ResidueColourFinder();
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
// everything is white if showBoxes is false
assertEquals(Color.white, rcf.getResidueColour(false,
{
SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
AlignmentI al = new Alignment(new SequenceI[] { seq });
- final AlignViewport av = new AlignViewport(al);
+ final AlignViewportI av = new AlignViewport(al);
ResidueColourFinder rcf = new ResidueColourFinder();
- assertEquals(Color.white,
- rcf.getResidueColour(true, av.getResidueShading(),
- null, seq, 0, null));
- assertEquals(Color.white,
- rcf.getResidueColour(true, av.getResidueShading(),
- null, seq, 2, null));
+ assertEquals(Color.white, rcf.getResidueColour(true,
+ av.getResidueShading(), null, seq, 0, null));
+ assertEquals(Color.white, rcf.getResidueColour(true,
+ av.getResidueShading(), null, seq, 2, null));
// no change if showBoxes is false
assertEquals(Color.white, rcf.getResidueColour(false,
SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
// gap
AlignmentI al = new Alignment(new SequenceI[] { seq });
- final AlignViewport av = new AlignViewport(al);
+ final AlignViewportI av = new AlignViewport(al);
ResidueColourFinder rcf = new ResidueColourFinder();
Color[] newColours = new Color[24];
// gap colour specified as pink
assertEquals(Color.pink, rcf.getResidueColour(true,
- av.getResidueShading(),
- null, seq, 3, null));
+ av.getResidueShading(), null, seq, 3, null));
// everything is white if showBoxes is false
newColours[23] = null;
assertEquals(Color.white, rcf.getResidueColour(false,
- av.getResidueShading(),
- null, seq, 3, null));
+ av.getResidueShading(), null, seq, 3, null));
newColours[23] = Color.pink;
av.setGlobalColourScheme(new UserColourScheme(newColours));