SequenceI seq = new Sequence("Seq1", "abcd");
AlignmentI al = new Alignment(new SequenceI[] { seq });
// the strings here correspond to JalviewColourScheme.toString() values
- assertTrue(ColourSchemeProperty.getColourScheme(al, "Clustal") instanceof ClustalxColourScheme);
+ ColourSchemeI cs = ColourSchemeProperty.getColourScheme(al, "Clustal");
+ assertTrue(cs instanceof ClustalxColourScheme);
// not case-sensitive
- assertTrue(ColourSchemeProperty.getColourScheme(al, "CLUSTAL") instanceof ClustalxColourScheme);
- assertTrue(ColourSchemeProperty.getColourScheme(al, "clustal") instanceof ClustalxColourScheme);
- assertTrue(ColourSchemeProperty.getColourScheme(al, "Blosum62") instanceof Blosum62ColourScheme);
- assertTrue(ColourSchemeProperty.getColourScheme(al, "% Identity") instanceof PIDColourScheme);
- assertTrue(ColourSchemeProperty.getColourScheme(al, "Zappo") instanceof ZappoColourScheme);
- assertTrue(ColourSchemeProperty.getColourScheme(al, "Taylor") instanceof TaylorColourScheme);
- assertTrue(ColourSchemeProperty.getColourScheme(al, "Hydrophobic") instanceof HydrophobicColourScheme);
- assertTrue(ColourSchemeProperty.getColourScheme(al, "Helix Propensity") instanceof HelixColourScheme);
- assertTrue(ColourSchemeProperty
- .getColourScheme(al, "Strand Propensity") instanceof StrandColourScheme);
- assertTrue(ColourSchemeProperty.getColourScheme(al, "Turn Propensity") instanceof TurnColourScheme);
- assertTrue(ColourSchemeProperty.getColourScheme(al, "Buried Index") instanceof BuriedColourScheme);
- assertTrue(ColourSchemeProperty.getColourScheme(al, "Nucleotide") instanceof NucleotideColourScheme);
- assertTrue(ColourSchemeProperty
- .getColourScheme(al, "Purine/Pyrimidine") instanceof PurinePyrimidineColourScheme);
- assertTrue(ColourSchemeProperty.getColourScheme(al, "T-Coffee Scores") instanceof TCoffeeColourScheme);
- assertTrue(ColourSchemeProperty.getColourScheme(al, "RNA Helices") instanceof RNAHelicesColour);
- assertTrue(ColourSchemeProperty.getColourScheme(al, "User Defined") instanceof UserColourScheme);
+ cs = ColourSchemeProperty.getColourScheme(al, "CLUSTAL");
+ assertTrue(cs instanceof ClustalxColourScheme);
+ cs = ColourSchemeProperty.getColourScheme(al, "clustal");
+ assertTrue(cs instanceof ClustalxColourScheme);
+ cs = ColourSchemeProperty.getColourScheme(al, "Blosum62");
+ assertTrue(cs instanceof Blosum62ColourScheme);
+ cs = ColourSchemeProperty.getColourScheme(al, "% Identity");
+ assertTrue(cs instanceof PIDColourScheme);
+ cs = ColourSchemeProperty.getColourScheme(al, "Zappo");
+ assertTrue(cs instanceof ZappoColourScheme);
+ cs = ColourSchemeProperty.getColourScheme(al, "Taylor");
+ assertTrue(cs instanceof TaylorColourScheme);
+ cs = ColourSchemeProperty.getColourScheme(al, "Hydrophobic");
+ assertTrue(cs instanceof HydrophobicColourScheme);
+ cs = ColourSchemeProperty.getColourScheme(al, "Helix Propensity");
+ assertTrue(cs instanceof HelixColourScheme);
+ cs = ColourSchemeProperty.getColourScheme(al, "Strand Propensity");
+ assertTrue(cs instanceof StrandColourScheme);
+ cs = ColourSchemeProperty.getColourScheme(al, "Turn Propensity");
+ assertTrue(cs instanceof TurnColourScheme);
+ cs = ColourSchemeProperty.getColourScheme(al, "Buried Index");
+ assertTrue(cs instanceof BuriedColourScheme);
+ cs = ColourSchemeProperty.getColourScheme(al, "Nucleotide");
+ assertTrue(cs instanceof NucleotideColourScheme);
+ cs = ColourSchemeProperty.getColourScheme(al, "Purine/Pyrimidine");
+ assertTrue(cs instanceof PurinePyrimidineColourScheme);
+ cs = ColourSchemeProperty.getColourScheme(al, "T-Coffee Scores");
+ assertTrue(cs instanceof TCoffeeColourScheme);
+ cs = ColourSchemeProperty.getColourScheme(al, "RNA Helices");
+ assertTrue(cs instanceof RNAHelicesColour);
// 'None' is a special value
assertNull(ColourSchemeProperty.getColourScheme(al, "None"));
assertNull(ColourSchemeProperty.getColourScheme(al, "none"));
// default is to convert the name into a fixed colour
- assertTrue(ColourSchemeProperty.getColourScheme(al, "elephants") instanceof UserColourScheme);
+ cs = ColourSchemeProperty.getColourScheme(al, "elephants");
+ assertTrue(cs instanceof UserColourScheme);
/*
* explicit aa colours
*/
- ColourSchemeI cs = ColourSchemeProperty.getColourScheme(al,
+ UserColourScheme ucs = (UserColourScheme) ColourSchemeProperty
+ .getColourScheme(al,
"R,G=red;C=blue;c=green;Q=10,20,30;S,T=11ffdd");
- assertEquals(cs.findColour('H'), Color.white);
- assertEquals(cs.findColour('R'), Color.red);
- assertEquals(cs.findColour('r'), Color.red);
- assertEquals(cs.findColour('G'), Color.red);
- assertEquals(cs.findColour('C'), Color.blue);
- assertEquals(cs.findColour('c'), Color.green);
- assertEquals(cs.findColour('Q'), new Color(10, 20, 30));
- assertEquals(cs.findColour('S'), new Color(0x11ffdd));
- assertEquals(cs.findColour('T'), new Color(0x11ffdd));
+ assertEquals(ucs.findColour('H'), Color.white);
+ assertEquals(ucs.findColour('R'), Color.red);
+ assertEquals(ucs.findColour('r'), Color.red);
+ assertEquals(ucs.findColour('G'), Color.red);
+ assertEquals(ucs.findColour('C'), Color.blue);
+ assertEquals(ucs.findColour('c'), Color.green);
+ assertEquals(ucs.findColour('Q'), new Color(10, 20, 30));
+ assertEquals(ucs.findColour('S'), new Color(0x11ffdd));
+ assertEquals(ucs.findColour('T'), new Color(0x11ffdd));
}
}