2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.schemes;
24 * An enum with the colour schemes supported by Jalview.
26 public enum JalviewColourScheme
29 * the order of declaration is the default order in which
30 * items are added to Colour menus
32 Clustal("Clustal", ClustalxColourScheme.class),
33 Blosum62("Blosum62", Blosum62ColourScheme.class),
34 PID("% Identity", PIDColourScheme.class),
35 Zappo("Zappo", ZappoColourScheme.class),
36 Taylor("Taylor", TaylorColourScheme.class),
37 Flower("gecos:flower", FlowerColourScheme.class),
38 Blossom("gecos:blossom", BlossomColourScheme.class),
39 Sunset("gecos:sunset", SunsetColourScheme.class),
40 Ocean("gecos:ocean", OceanColourScheme.class),
41 Hydrophobic("Hydrophobic", HydrophobicColourScheme.class),
42 Helix("Helix Propensity", HelixColourScheme.class),
43 Strand("Strand Propensity", StrandColourScheme.class),
44 Turn("Turn Propensity", TurnColourScheme.class),
45 Buried("Buried Index", BuriedColourScheme.class),
46 Nucleotide("Nucleotide", NucleotideColourScheme.class),
47 PurinePyrimidine("Purine/Pyrimidine", PurinePyrimidineColourScheme.class),
48 RNAHelices("RNA Helices", RNAHelicesColour.class),
49 TCoffee("T-Coffee Scores", TCoffeeColourScheme.class),
50 IdColour("Sequence ID", IdColourScheme.class),
51 HMMERU("HMMER-Uniprot", HmmerGlobalBackground.class),
52 HMMERA("HMMER-Alignment", HmmerLocalBackground.class),
53 HMMMatchScore("HMM Match Score", HMMMatchScoreColourScheme.class);
54 // RNAInteraction("RNA Interaction type", RNAInteractionColourScheme.class)
58 private Class<? extends ColourSchemeI> myClass;
61 * Constructor given the name of the colour scheme (as used in Jalview
62 * parameters). Note this is not necessarily the same as the 'display name'
63 * used in menu options (as this may be language-dependent).
67 JalviewColourScheme(String s, Class<? extends ColourSchemeI> cl)
74 * Returns the class of the colour scheme
78 public Class<? extends ColourSchemeI> getSchemeClass()
84 * Returns the 'official' name of this colour scheme. This is the name that
85 * identifies the colour scheme as a start-up parameter for the Jalview
86 * application or applet. Note that it may not be the name shown in menu
87 * options, as these may be internationalised.
90 public String toString()