+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.schemes;
import static org.testng.Assert.assertEquals;
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(null, 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(null, al, "CLUSTAL");
+ assertTrue(cs instanceof ClustalxColourScheme);
+ cs = ColourSchemeProperty.getColourScheme(null, al, "clustal");
+ assertTrue(cs instanceof ClustalxColourScheme);
+ cs = ColourSchemeProperty.getColourScheme(null, al, "Blosum62");
+ assertTrue(cs instanceof Blosum62ColourScheme);
+ cs = ColourSchemeProperty.getColourScheme(null, al, "% Identity");
+ assertTrue(cs instanceof PIDColourScheme);
+ cs = ColourSchemeProperty.getColourScheme(null, al, "Zappo");
+ assertTrue(cs instanceof ZappoColourScheme);
+ cs = ColourSchemeProperty.getColourScheme(null, al, "Taylor");
+ assertTrue(cs instanceof TaylorColourScheme);
+ cs = ColourSchemeProperty.getColourScheme(null, al, "Hydrophobic");
+ assertTrue(cs instanceof HydrophobicColourScheme);
+ cs = ColourSchemeProperty.getColourScheme(null, al, "Helix Propensity");
+ assertTrue(cs instanceof HelixColourScheme);
+ cs = ColourSchemeProperty.getColourScheme(null, al,
+ "Strand Propensity");
+ assertTrue(cs instanceof StrandColourScheme);
+ cs = ColourSchemeProperty.getColourScheme(null, al, "Turn Propensity");
+ assertTrue(cs instanceof TurnColourScheme);
+ cs = ColourSchemeProperty.getColourScheme(null, al, "Buried Index");
+ assertTrue(cs instanceof BuriedColourScheme);
+ cs = ColourSchemeProperty.getColourScheme(null, al, "Nucleotide");
+ assertTrue(cs instanceof NucleotideColourScheme);
+ cs = ColourSchemeProperty.getColourScheme(null, al,
+ "Purine/Pyrimidine");
+ assertTrue(cs instanceof PurinePyrimidineColourScheme);
+ cs = ColourSchemeProperty.getColourScheme(null, al, "T-Coffee Scores");
+ assertTrue(cs instanceof TCoffeeColourScheme);
+ 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
- assertTrue(ColourSchemeProperty.getColourScheme(al, "elephants") instanceof UserColourScheme);
+ cs = ColourSchemeProperty.getColourScheme(null, al, "elephants");
+ assertTrue(cs instanceof UserColourScheme);
/*
* explicit aa colours
*/
- UserColourScheme cs = (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));
+ UserColourScheme ucs = (UserColourScheme) ColourSchemeProperty
+ .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);
+ 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));
}
}