2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.schemes;
20 import jalview.datamodel.AnnotatedCollectionI;
22 import java.awt.Color;
25 * ColourSchemeProperty binds names to hardwired colourschemes and tries to deal
26 * intelligently with mapping unknown names to user defined colourschemes (that
27 * exist or can be created from the string representation of the colourscheme
28 * name - either a hex RGB triplet or a named colour under java.awt.color ). The
29 * values of the colourscheme constants is important for callers of
30 * getColourName(int i), since it can be used to enumerate the set of built in
31 * colours. The FIRST_COLOUR and LAST_COLOUR symbols are provided for this.
36 public class ColourSchemeProperty
38 /** Undefined Colourscheme Index */
39 public static final int UNDEFINED = -1;
41 /** for schemes defined on the fly */
42 public static final int USER_DEFINED = 0;
44 /** No Colourscheme Index */
45 public static final int NONE = 1;
48 public static final int CLUSTAL = 2;
51 public static final int BLOSUM = 3;
54 public static final int PID = 4;
57 public static final int ZAPPO = 5;
60 public static final int TAYLOR = 6;
63 public static final int HYDROPHOBIC = 7;
66 public static final int HELIX = 8;
69 public static final int STRAND = 9;
72 public static final int TURN = 10;
75 public static final int BURIED = 11;
78 public static final int NUCLEOTIDE = 12;
83 public static final int PURINEPYRIMIDINE = 13;
85 public static final int COVARIATION = 14;
87 public static final int TCOFFEE = 15;
91 * index of first colourscheme (includes 'None')
93 public static final int FIRST_COLOUR = NONE;
95 public static final int LAST_COLOUR = NUCLEOTIDE;
103 * @return DOCUMENT ME!
105 public static int getColourIndexFromName(String name)
109 if (name.equalsIgnoreCase("Clustal"))
113 else if (name.equalsIgnoreCase("Blosum62"))
117 else if (name.equalsIgnoreCase("% Identity"))
121 else if (name.equalsIgnoreCase("Zappo"))
125 else if (name.equalsIgnoreCase("Taylor"))
129 else if (name.equalsIgnoreCase("Hydrophobic"))
133 else if (name.equalsIgnoreCase("Helix Propensity"))
137 else if (name.equalsIgnoreCase("Strand Propensity"))
141 else if (name.equalsIgnoreCase("Turn Propensity"))
145 else if (name.equalsIgnoreCase("Buried Index"))
149 else if (name.equalsIgnoreCase("Nucleotide"))
153 else if (name.equalsIgnoreCase("T-Coffee Scores"))
158 else if (name.equalsIgnoreCase("User Defined"))
162 else if (name.equalsIgnoreCase("None"))
166 else if (name.equalsIgnoreCase("Purine/Pyrimidine"))
168 ret = PURINEPYRIMIDINE;
170 // else if (name.equalsIgnoreCase("Covariation"))
172 // ret = COVARIATION;
184 * @return DOCUMENT ME!
186 public static String getColourName(ColourSchemeI cs)
191 if (cs instanceof ClustalxColourScheme)
195 else if (cs instanceof Blosum62ColourScheme)
199 else if (cs instanceof PIDColourScheme)
203 else if (cs instanceof ZappoColourScheme)
207 else if (cs instanceof TaylorColourScheme)
211 else if (cs instanceof HydrophobicColourScheme)
215 else if (cs instanceof HelixColourScheme)
219 else if (cs instanceof StrandColourScheme)
223 else if (cs instanceof TurnColourScheme)
227 else if (cs instanceof BuriedColourScheme)
231 else if (cs instanceof NucleotideColourScheme)
235 else if (cs instanceof PurinePyrimidineColourScheme)
237 index = PURINEPYRIMIDINE;
239 else if (cs instanceof TCoffeeColourScheme)
244 * else if (cs instanceof CovariationColourScheme) { index = COVARIATION; }
246 else if (cs instanceof UserColourScheme)
248 if ((((UserColourScheme) cs).getName() != null)
249 && (((UserColourScheme) cs).getName().length() > 0))
251 return ((UserColourScheme) cs).getName();
253 // get default colourscheme name
254 index = USER_DEFINED;
257 return getColourName(index);
266 * @return DOCUMENT ME!
268 public static String getColourName(int index)
304 ret = "Helix Propensity";
309 ret = "Strand Propensity";
314 ret = "Turn Propensity";
319 ret = "Buried Index";
328 case PURINEPYRIMIDINE:
329 ret = "Purine/Pyrimidine";
334 ret = "T-Coffee Scores";
338 * case COVARIATION: ret = "Covariation";
343 ret = "User Defined";
356 * retrieve or create colourscheme associated with name
359 * sequences to colour
361 * range of sequences to colour
363 * colourscheme name, applet colour parameter specification, or
364 * string to parse as colour for new coloursheme
365 * @return Valid Colourscheme
367 public static ColourSchemeI getColour(AnnotatedCollectionI alignment,
370 int colindex = getColourIndexFromName(name);
371 if (colindex == UNDEFINED)
373 if (name.indexOf('=') == -1)
375 // try to build a colour from the string directly
378 return new UserColourScheme(name);
379 } catch (Exception e)
381 // System.err.println("Ignoring unknown colourscheme name");
386 // try to parse the string as a residue colourscheme
389 // fix the launchApp user defined coloursheme transfer bug
390 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
392 ucs.parseAppletParameter(name);
394 } catch (Exception e)
396 // System.err.println("Ignoring exception when parsing colourscheme as applet-parameter");
400 return getColour(alignment, getColourIndexFromName(name));
404 * Construct an instance of ColourSchemeI corresponding to the given colourscheme index
407 * sequences to be coloured by colourscheme
409 * geometry of alignment
411 * colourscheme number
413 * @return null or an instance of the colourscheme configured to colour given sequence set
415 public static ColourSchemeI getColour(jalview.datamodel.AnnotatedCollectionI coll, int index)
417 // TODO 3.0 2.8 refactor signature to take an alignmentI like container so colourschemes based on annotation can be initialised
418 ColourSchemeI cs = null;
423 cs = new ClustalxColourScheme(coll, null);
428 cs = new Blosum62ColourScheme();
433 cs = new PIDColourScheme();
438 cs = new ZappoColourScheme();
443 cs = new TaylorColourScheme();
447 cs = new HydrophobicColourScheme();
452 cs = new HelixColourScheme();
457 cs = new StrandColourScheme();
462 cs = new TurnColourScheme();
467 cs = new BuriedColourScheme();
472 cs = new NucleotideColourScheme();
476 case PURINEPYRIMIDINE:
477 cs = new PurinePyrimidineColourScheme();
482 cs = new TCoffeeColourScheme(coll);
484 // cs = new CovariationColourScheme(annotation);
489 Color[] col = new Color[24];
490 for (int i = 0; i < 24; i++)
492 col[i] = Color.white;
494 cs = new UserColourScheme(col);
504 public static Color getAWTColorFromName(String name)
507 name = name.toLowerCase();
508 if (name.equals("black"))
512 else if (name.equals("blue"))
516 else if (name.equals("cyan"))
520 else if (name.equals("darkGray"))
522 col = Color.darkGray;
524 else if (name.equals("gray"))
528 else if (name.equals("green"))
532 else if (name.equals("lightGray"))
534 col = Color.lightGray;
536 else if (name.equals("magenta"))
540 else if (name.equals("orange"))
544 else if (name.equals("pink"))
548 else if (name.equals("red"))
552 else if (name.equals("white"))
556 else if (name.equals("yellow"))