+
+ @Test(groups = "Functional")
+ public void testGetColourScheme_forViewport()
+ {
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ ">seq1\nAGLRTWQU", DataSourceType.PASTE);
+ ColourSchemes cs = ColourSchemes.getInstance();
+
+ AlignViewport viewport = af.getViewport();
+ assertTrue(cs.getColourScheme(JalviewColourScheme.Blosum62.toString(),
+ viewport) instanceof Blosum62ColourScheme);
+ assertTrue(cs.getColourScheme(JalviewColourScheme.Buried.toString(),
+ viewport) instanceof BuriedColourScheme);
+ assertTrue(cs.getColourScheme(JalviewColourScheme.Clustal.toString(),
+ viewport) instanceof ClustalxColourScheme);
+ assertTrue(cs.getColourScheme(JalviewColourScheme.Helix.toString(),
+ viewport) instanceof HelixColourScheme);
+ assertTrue(cs.getColourScheme(
+ JalviewColourScheme.Hydrophobic.toString(), viewport) instanceof HydrophobicColourScheme);
+ assertTrue(cs.getColourScheme(
+ JalviewColourScheme.Nucleotide.toString(), viewport) instanceof NucleotideColourScheme);
+ assertTrue(cs.getColourScheme(JalviewColourScheme.PID.toString(),
+ viewport) instanceof PIDColourScheme);
+ assertTrue(cs.getColourScheme(
+ JalviewColourScheme.PurinePyrimidine.toString(), viewport) instanceof PurinePyrimidineColourScheme);
+ assertTrue(cs.getColourScheme(
+ JalviewColourScheme.RNAHelices.toString(), viewport) instanceof RNAHelicesColour);
+ assertTrue(cs.getColourScheme(JalviewColourScheme.Strand.toString(),
+ viewport) instanceof StrandColourScheme);
+ assertTrue(cs.getColourScheme(JalviewColourScheme.Taylor.toString(),
+ viewport) instanceof TaylorColourScheme);
+ assertTrue(cs.getColourScheme(JalviewColourScheme.TCoffee.toString(),
+ viewport) instanceof TCoffeeColourScheme);
+ assertTrue(cs.getColourScheme(JalviewColourScheme.Turn.toString(),
+ viewport) instanceof TurnColourScheme);
+ assertTrue(cs.getColourScheme(JalviewColourScheme.Zappo.toString(),
+ viewport) instanceof ZappoColourScheme);
+ af.closeMenuItem_actionPerformed(true);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetColourScheme_forAnnotatedCollection()
+ {
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ ">seq1\nAGLRTWQU", DataSourceType.PASTE);
+ ColourSchemes cs = 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);
+ af.closeMenuItem_actionPerformed(true);
+ }
+
+ @Test(groups = "Functional")
+ public void testRegisterColourScheme()
+ {
+ ColourSchemes.getInstance().registerColourScheme(new Stripy());
+ ColourSchemes.getInstance().registerColourScheme(new MyClustal());
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.fa", DataSourceType.FILE);
+ /*
+ * set a breakpoint here to see and play with the newly registered
+ * colour schemes in the AlignFrame colour menu
+ */
+ SequenceRenderer sr = new SequenceRenderer(af.getViewport());
+ SequenceI seq = af.getViewport().getAlignment().findName("FER_CAPAA");
+
+ /*
+ * set and check Taylor colours
+ */
+ af.changeColour_actionPerformed(JalviewColourScheme.Taylor.toString());
+ Color taylor1 = sr.getResidueBoxColour(seq, 88); // E 255,0,102
+ Color taylor2 = sr.getResidueBoxColour(seq, 89); // A 204,255,0
+ Color taylor3 = sr.getResidueBoxColour(seq, 90); // G 255,153,0
+ assertEquals(taylor1, new Color(255, 0, 102));
+ assertEquals(taylor2, new Color(204, 255, 0));
+ assertEquals(taylor3, new Color(255, 153, 0));
+
+ /*
+ * set and check Zappo colours
+ */
+ af.changeColour_actionPerformed(JalviewColourScheme.Zappo.toString());
+ Color zappo1 = sr.getResidueBoxColour(seq, 88); // E red
+ Color zappo2 = sr.getResidueBoxColour(seq, 89); // A pink
+ Color zappo3 = sr.getResidueBoxColour(seq, 90); // G magenta
+ assertEquals(zappo1, Color.red);
+ assertEquals(zappo2, Color.pink);
+ assertEquals(zappo3, Color.magenta);
+
+ /*
+ * set 'stripy' colours - odd columns are Taylor and even are Zappo
+ */
+ af.changeColour_actionPerformed("stripy");
+ Color stripy1 = sr.getResidueBoxColour(seq, 88);
+ Color stripy2 = sr.getResidueBoxColour(seq, 89);
+ Color stripy3 = sr.getResidueBoxColour(seq, 90);
+ assertEquals(stripy1, zappo1);
+ assertEquals(stripy2, taylor2);
+ assertEquals(stripy3, zappo3);
+
+ /*
+ * set and check Clustal colours
+ */
+ af.changeColour_actionPerformed(JalviewColourScheme.Clustal.toString());
+ Color clustal1 = sr.getResidueBoxColour(seq, 88);
+ Color clustal2 = sr.getResidueBoxColour(seq, 89);
+ Color clustal3 = sr.getResidueBoxColour(seq, 90);
+ assertEquals(clustal1, ClustalColour.MAGENTA.colour);
+ assertEquals(clustal2, ClustalColour.BLUE.colour);
+ assertEquals(clustal3, ClustalColour.ORANGE.colour);
+
+ /*
+ * set 'MyClustal' colours - uses AWT colour equivalents
+ */
+ af.changeColour_actionPerformed("MyClustal");
+ Color myclustal1 = sr.getResidueBoxColour(seq, 88);
+ Color myclustal2 = sr.getResidueBoxColour(seq, 89);
+ Color myclustal3 = sr.getResidueBoxColour(seq, 90);
+ assertEquals(myclustal1, Color.MAGENTA);
+ assertEquals(myclustal2, Color.BLUE);
+ assertEquals(myclustal3, Color.ORANGE);
+ }