package jalview.schemes;
import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertSame;
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;
import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
import jalview.gui.Desktop;
import jalview.gui.SequenceRenderer;
import jalview.io.DataSourceType;
*/
class Stripy extends ResidueColourScheme
{
- private ColourSchemeI odd;
+ private ResidueColourScheme odd;
- private ColourSchemeI even;
+ private ResidueColourScheme even;
private Stripy()
{
*/
private Stripy(ColourSchemeI cs1, ColourSchemeI cs2)
{
- odd = cs1;
- even = cs2;
+ odd = (ResidueColourScheme) cs1;
+ even = (ResidueColourScheme) cs2;
}
@Override
*/
class MyClustal extends ResidueColourScheme
{
- ColourSchemeI delegate;
+ ClustalxColourScheme delegate;
private MyClustal()
{
}
- private MyClustal(ColourSchemeI scheme)
+ private MyClustal(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
- delegate = scheme;
+ delegate = new ClustalxColourScheme(sg, hiddenRepSequences);
}
@Override
public ColourSchemeI getInstance(AnnotatedCollectionI sg,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
- return new MyClustal(new ClustalxColourScheme().getInstance(sg,
- hiddenRepSequences));
+ return new MyClustal(sg, hiddenRepSequences);
}
@Override
}
@Test(groups = "Functional")
- public void testGetColourScheme_forViewport()
- {
- AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
- ">seq1\nAGLRTWQU", DataSourceType.PASTE);
- ColourSchemes cs = ColourSchemes.getInstance();
-
- AlignViewport viewport = af.getViewport();
- AlignmentI alignment = viewport.getAlignment();
- assertTrue(cs.getColourScheme(JalviewColourScheme.Blosum62.toString(),
- alignment) instanceof Blosum62ColourScheme);
- assertTrue(cs.getColourScheme(JalviewColourScheme.Buried.toString(),
- alignment) instanceof BuriedColourScheme);
- assertTrue(cs.getColourScheme(JalviewColourScheme.Clustal.toString(),
- alignment) instanceof ClustalxColourScheme);
- assertTrue(cs.getColourScheme(JalviewColourScheme.Helix.toString(),
- alignment) instanceof HelixColourScheme);
- assertTrue(cs.getColourScheme(
- JalviewColourScheme.Hydrophobic.toString(), alignment) instanceof HydrophobicColourScheme);
- assertTrue(cs.getColourScheme(
- JalviewColourScheme.Nucleotide.toString(), alignment) instanceof NucleotideColourScheme);
- assertTrue(cs.getColourScheme(JalviewColourScheme.PID.toString(),
- alignment) instanceof PIDColourScheme);
- assertTrue(cs.getColourScheme(
- JalviewColourScheme.PurinePyrimidine.toString(), alignment) instanceof PurinePyrimidineColourScheme);
- assertTrue(cs.getColourScheme(
- JalviewColourScheme.RNAHelices.toString(), alignment) instanceof RNAHelicesColour);
- assertTrue(cs.getColourScheme(JalviewColourScheme.Strand.toString(),
- alignment) instanceof StrandColourScheme);
- assertTrue(cs.getColourScheme(JalviewColourScheme.Taylor.toString(),
- alignment) instanceof TaylorColourScheme);
- assertTrue(cs.getColourScheme(JalviewColourScheme.TCoffee.toString(),
- alignment) instanceof TCoffeeColourScheme);
- assertTrue(cs.getColourScheme(JalviewColourScheme.Turn.toString(),
- alignment) instanceof TurnColourScheme);
- assertTrue(cs.getColourScheme(JalviewColourScheme.Zappo.toString(),
- alignment) instanceof ZappoColourScheme);
- af.closeMenuItem_actionPerformed(true);
- }
-
- @Test(groups = "Functional")
- public void testGetColourScheme_forAnnotatedCollection()
+ public void testGetColourScheme()
{
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
">seq1\nAGLRTWQU", DataSourceType.PASTE);
- ColourSchemes cs = ColourSchemes.getInstance();
+ ColourSchemes schemes = ColourSchemes.getInstance();
AnnotatedCollectionI al = af.getViewport().getAlignment();
- assertTrue(cs.getColourScheme(JalviewColourScheme.Blosum62.toString(),
- al) instanceof Blosum62ColourScheme);
- assertTrue(cs
- .getColourScheme(JalviewColourScheme.Buried.toString(), al) instanceof BuriedColourScheme);
- assertTrue(cs.getColourScheme(JalviewColourScheme.Clustal.toString(),
- al) instanceof ClustalxColourScheme);
- assertTrue(cs.getColourScheme(JalviewColourScheme.Helix.toString(), al) instanceof HelixColourScheme);
- assertTrue(cs.getColourScheme(
- JalviewColourScheme.Hydrophobic.toString(), al) instanceof HydrophobicColourScheme);
- assertTrue(cs.getColourScheme(
- JalviewColourScheme.Nucleotide.toString(), al) instanceof NucleotideColourScheme);
- assertTrue(cs.getColourScheme(JalviewColourScheme.PID.toString(), al) instanceof PIDColourScheme);
- assertTrue(cs.getColourScheme(
- JalviewColourScheme.PurinePyrimidine.toString(), al) instanceof PurinePyrimidineColourScheme);
- assertTrue(cs.getColourScheme(
- JalviewColourScheme.RNAHelices.toString(), al) instanceof RNAHelicesColour);
- assertTrue(cs
- .getColourScheme(JalviewColourScheme.Strand.toString(), al) instanceof StrandColourScheme);
- assertTrue(cs
- .getColourScheme(JalviewColourScheme.Taylor.toString(), al) instanceof TaylorColourScheme);
- assertTrue(cs.getColourScheme(JalviewColourScheme.TCoffee.toString(),
- al) instanceof TCoffeeColourScheme);
- assertTrue(cs.getColourScheme(JalviewColourScheme.Turn.toString(), al) instanceof TurnColourScheme);
- assertTrue(cs.getColourScheme(JalviewColourScheme.Zappo.toString(), al) instanceof ZappoColourScheme);
+
+ for (JalviewColourScheme cs : JalviewColourScheme.values())
+ {
+ ColourSchemeI registered = schemes.getColourScheme(cs.toString(), al);
+ assertSame(registered.getClass(), cs.getSchemeClass());
+ }
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"));
+ }
}