package jalview.schemes;
import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
import static org.testng.Assert.assertTrue;
import jalview.bin.Cache;
import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
*/
class Stripy extends ResidueColourScheme
{
+ private ColourSchemeI odd;
+
+ private ColourSchemeI even;
+
+ private Stripy()
+ {
+ }
+
+ /**
+ * constructor given colours for odd and even columns
+ *
+ * @param odd
+ * @param even
+ */
+ private Stripy(ColourSchemeI cs1, ColourSchemeI cs2)
+ {
+ odd = cs1;
+ even = cs2;
+ }
+
@Override
public ColourSchemeI getInstance(AnnotatedCollectionI sg,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
- final ColourSchemeI odd = ColourSchemes.getInstance()
+ final ColourSchemeI cs1 = ColourSchemes.getInstance()
.getColourScheme(JalviewColourScheme.Taylor.toString(),
(AnnotatedCollectionI) null);
- final ColourSchemeI even = ColourSchemes.getInstance()
+ final ColourSchemeI cs2 = ColourSchemes.getInstance()
.getColourScheme(JalviewColourScheme.Zappo.toString(),
(AnnotatedCollectionI) null);
- return new ResidueColourScheme() {
- @Override
- public Color findColour(char c, int j, SequenceI seq)
- {
- if (j % 2 == 1)
- {
- return odd.findColour(c, j, seq);
- }
- else
- {
- return even.findColour(c, j, seq);
- }
- }
-
- @Override
- public ColourSchemeI getInstance(AnnotatedCollectionI sg,
- Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
- {
- return null;
- }
+ return new Stripy(cs1, cs2);
+ }
- @Override
- public String getSchemeName()
- {
- return Stripy.this.getSchemeName();
- }
-
- };
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
+ {
+ if (j % 2 == 1)
+ {
+ return odd.findColour(c, j, seq);
+ }
+ else
+ {
+ return even.findColour(c, j, seq);
+ }
}
-
+
@Override
public String getSchemeName()
{
{
ColourSchemeI delegate;
- public MyClustal()
+ private MyClustal()
{
}
- public MyClustal(ColourSchemeI scheme)
+ private MyClustal(ColourSchemeI scheme)
{
delegate = scheme;
}
ColourSchemes cs = ColourSchemes.getInstance();
AlignViewport viewport = af.getViewport();
+ AlignmentI alignment = viewport.getAlignment();
assertTrue(cs.getColourScheme(JalviewColourScheme.Blosum62.toString(),
- viewport) instanceof Blosum62ColourScheme);
+ alignment) instanceof Blosum62ColourScheme);
assertTrue(cs.getColourScheme(JalviewColourScheme.Buried.toString(),
- viewport) instanceof BuriedColourScheme);
+ alignment) instanceof BuriedColourScheme);
assertTrue(cs.getColourScheme(JalviewColourScheme.Clustal.toString(),
- viewport) instanceof ClustalxColourScheme);
+ alignment) instanceof ClustalxColourScheme);
assertTrue(cs.getColourScheme(JalviewColourScheme.Helix.toString(),
- viewport) instanceof HelixColourScheme);
+ alignment) instanceof HelixColourScheme);
assertTrue(cs.getColourScheme(
- JalviewColourScheme.Hydrophobic.toString(), viewport) instanceof HydrophobicColourScheme);
+ JalviewColourScheme.Hydrophobic.toString(), alignment) instanceof HydrophobicColourScheme);
assertTrue(cs.getColourScheme(
- JalviewColourScheme.Nucleotide.toString(), viewport) instanceof NucleotideColourScheme);
+ JalviewColourScheme.Nucleotide.toString(), alignment) instanceof NucleotideColourScheme);
assertTrue(cs.getColourScheme(JalviewColourScheme.PID.toString(),
- viewport) instanceof PIDColourScheme);
+ alignment) instanceof PIDColourScheme);
assertTrue(cs.getColourScheme(
- JalviewColourScheme.PurinePyrimidine.toString(), viewport) instanceof PurinePyrimidineColourScheme);
+ JalviewColourScheme.PurinePyrimidine.toString(), alignment) instanceof PurinePyrimidineColourScheme);
assertTrue(cs.getColourScheme(
- JalviewColourScheme.RNAHelices.toString(), viewport) instanceof RNAHelicesColour);
+ JalviewColourScheme.RNAHelices.toString(), alignment) instanceof RNAHelicesColour);
assertTrue(cs.getColourScheme(JalviewColourScheme.Strand.toString(),
- viewport) instanceof StrandColourScheme);
+ alignment) instanceof StrandColourScheme);
assertTrue(cs.getColourScheme(JalviewColourScheme.Taylor.toString(),
- viewport) instanceof TaylorColourScheme);
+ alignment) instanceof TaylorColourScheme);
assertTrue(cs.getColourScheme(JalviewColourScheme.TCoffee.toString(),
- viewport) instanceof TCoffeeColourScheme);
+ alignment) instanceof TCoffeeColourScheme);
assertTrue(cs.getColourScheme(JalviewColourScheme.Turn.toString(),
- viewport) instanceof TurnColourScheme);
+ alignment) instanceof TurnColourScheme);
assertTrue(cs.getColourScheme(JalviewColourScheme.Zappo.toString(),
- viewport) instanceof ZappoColourScheme);
+ alignment) instanceof ZappoColourScheme);
af.closeMenuItem_actionPerformed(true);
}
assertEquals(myclustal2, Color.BLUE);
assertEquals(myclustal3, Color.ORANGE);
}
+
+ /**
+ * Tests for check if scheme name exists. Built-in scheme names are the
+ * toString() values of enum JalviewColourScheme.
+ */
+ @Test(groups = "Functional")
+ public void testNameExists()
+ {
+ ColourSchemes cs = ColourSchemes.getInstance();
+ assertFalse(cs.nameExists(null));
+ assertFalse(cs.nameExists(""));
+ assertTrue(cs.nameExists("Clustal"));
+ assertTrue(cs.nameExists("CLUSTAL"));
+ assertFalse(cs.nameExists("CLUSTAL "));
+ assertTrue(cs.nameExists("% Identity"));
+ assertFalse(cs.nameExists("PID"));
+ }
}