SequenceI seq = new Sequence("Seq1", "abcd");
AlignmentI al = new Alignment(new SequenceI[] { seq });
// the strings here correspond to JalviewColourScheme.toString() values
- ColourSchemeI cs = ColourSchemeProperty.getColourScheme(al, "Clustal");
+ ColourSchemeI cs = ColourSchemeProperty.getColourScheme(null, al,
+ "Clustal");
assertTrue(cs instanceof ClustalxColourScheme);
// not case-sensitive
- cs = ColourSchemeProperty.getColourScheme(al, "CLUSTAL");
+ cs = ColourSchemeProperty.getColourScheme(null, al, "CLUSTAL");
assertTrue(cs instanceof ClustalxColourScheme);
- cs = ColourSchemeProperty.getColourScheme(al, "clustal");
+ cs = ColourSchemeProperty.getColourScheme(null, al, "clustal");
assertTrue(cs instanceof ClustalxColourScheme);
- cs = ColourSchemeProperty.getColourScheme(al, "Blosum62");
+ cs = ColourSchemeProperty.getColourScheme(null, al, "Blosum62");
assertTrue(cs instanceof Blosum62ColourScheme);
- cs = ColourSchemeProperty.getColourScheme(al, "% Identity");
+ cs = ColourSchemeProperty.getColourScheme(null, al, "% Identity");
assertTrue(cs instanceof PIDColourScheme);
- cs = ColourSchemeProperty.getColourScheme(al, "Zappo");
+ cs = ColourSchemeProperty.getColourScheme(null, al, "Zappo");
assertTrue(cs instanceof ZappoColourScheme);
- cs = ColourSchemeProperty.getColourScheme(al, "Taylor");
+ cs = ColourSchemeProperty.getColourScheme(null, al, "Taylor");
assertTrue(cs instanceof TaylorColourScheme);
- cs = ColourSchemeProperty.getColourScheme(al, "Hydrophobic");
+ cs = ColourSchemeProperty.getColourScheme(null, al, "Hydrophobic");
assertTrue(cs instanceof HydrophobicColourScheme);
- cs = ColourSchemeProperty.getColourScheme(al, "Helix Propensity");
+ cs = ColourSchemeProperty.getColourScheme(null, al, "Helix Propensity");
assertTrue(cs instanceof HelixColourScheme);
- cs = ColourSchemeProperty.getColourScheme(al, "Strand Propensity");
+ cs = ColourSchemeProperty.getColourScheme(null, al,
+ "Strand Propensity");
assertTrue(cs instanceof StrandColourScheme);
- cs = ColourSchemeProperty.getColourScheme(al, "Turn Propensity");
+ cs = ColourSchemeProperty.getColourScheme(null, al, "Turn Propensity");
assertTrue(cs instanceof TurnColourScheme);
- cs = ColourSchemeProperty.getColourScheme(al, "Buried Index");
+ cs = ColourSchemeProperty.getColourScheme(null, al, "Buried Index");
assertTrue(cs instanceof BuriedColourScheme);
- cs = ColourSchemeProperty.getColourScheme(al, "Nucleotide");
+ cs = ColourSchemeProperty.getColourScheme(null, al, "Nucleotide");
assertTrue(cs instanceof NucleotideColourScheme);
- cs = ColourSchemeProperty.getColourScheme(al, "Purine/Pyrimidine");
+ cs = ColourSchemeProperty.getColourScheme(null, al,
+ "Purine/Pyrimidine");
assertTrue(cs instanceof PurinePyrimidineColourScheme);
- cs = ColourSchemeProperty.getColourScheme(al, "T-Coffee Scores");
+ cs = ColourSchemeProperty.getColourScheme(null, al, "T-Coffee Scores");
assertTrue(cs instanceof TCoffeeColourScheme);
- cs = ColourSchemeProperty.getColourScheme(al, "RNA Helices");
+ cs = ColourSchemeProperty.getColourScheme(null, al, "RNA Helices");
assertTrue(cs instanceof RNAHelicesColour);
// 'None' is a special value
- assertNull(ColourSchemeProperty.getColourScheme(al, "None"));
- assertNull(ColourSchemeProperty.getColourScheme(al, "none"));
+ assertNull(ColourSchemeProperty.getColourScheme(null, al, "None"));
+ assertNull(ColourSchemeProperty.getColourScheme(null, al, "none"));
// default is to convert the name into a fixed colour
- cs = ColourSchemeProperty.getColourScheme(al, "elephants");
+ cs = ColourSchemeProperty.getColourScheme(null, al, "elephants");
assertTrue(cs instanceof UserColourScheme);
/*
* explicit aa colours
*/
UserColourScheme ucs = (UserColourScheme) ColourSchemeProperty
- .getColourScheme(al,
+ .getColourScheme(null, al,
"R,G=red;C=blue;c=green;Q=10,20,30;S,T=11ffdd");
assertEquals(ucs.findColour('H'), Color.white);
assertEquals(ucs.findColour('R'), Color.red);