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;
23 import jalview.api.AlignViewportI;
24 import jalview.datamodel.AnnotatedCollectionI;
27 * ColourSchemeProperty binds names to hardwired colourschemes and tries to deal
28 * intelligently with mapping unknown names to user defined colourschemes (that
29 * exist or can be created from the string representation of the colourscheme
30 * name - either a hex RGB triplet or a named colour under java.awt.color ). The
31 * values of the colourscheme constants is important for callers of
32 * getColourName(int i), since it can be used to enumerate the set of built in
33 * colours. The FIRST_COLOUR and LAST_COLOUR symbols are provided for this.
38 public class ColourSchemeProperty
41 private ColourSchemeProperty()
43 // requires static call to getColourScheme(...).
47 * Returns a colour scheme for the given name, with which the given data may
48 * be coloured. The name is not case-sensitive, and may be one of
50 * <li>any currently registered colour scheme; Jalview by default
56 * <li>Hydrophobic</li>
59 * <li>Helix Propensity</li>
60 * <li>Strand Propensity</li>
61 * <li>Turn Propensity</li>
62 * <li>Buried Index</li>
64 * <li>Purine/Pyrimidine</li>
65 * <li>T-Coffee Scores</li>
66 * <li>RNA Helices</li>
68 * <li>the name of a programmatically added colour scheme</li>
69 * <li>an AWT colour name e.g. red</li>
70 * <li>an AWT hex rgb colour e.g. ff2288</li>
71 * <li>residue colours list e.g. D,E=red;K,R,H=0022FF;c=yellow</li>
74 * If none of these formats is matched, the string is converted to a colour
75 * using a hashing algorithm. For name "None", returns null.
81 public static ColourSchemeI getColourScheme(AlignViewportI view,
82 AnnotatedCollectionI forData,
85 if (ResidueColourScheme.NONE.equalsIgnoreCase(name))
92 * if this is the name of a registered colour scheme, just
93 * create a new instance of it
95 ColourSchemeI scheme = ColourSchemes.getInstance().getColourScheme(name,
104 * try to parse the string as a residues colour scheme
105 * e.g. A=red;T,G=blue etc
106 * else parse the name as a colour specification
107 * e.g. "red" or "ff00ed",
108 * or failing that hash the name to a colour
110 UserColourScheme ucs = new UserColourScheme(name);
115 * Returns the name of the colour scheme (or "None" if it is null)
120 public static String getColourName(ColourSchemeI cs)
122 return cs == null ? ResidueColourScheme.NONE : cs.getSchemeName();