2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
3 * Copyright (C) 2014 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 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/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
19 package jalview.schemes;
21 import jalview.datamodel.AnnotatedCollectionI;
23 import java.awt.Color;
26 * ColourSchemeProperty binds names to hardwired colourschemes and tries to deal
27 * intelligently with mapping unknown names to user defined colourschemes (that
28 * exist or can be created from the string representation of the colourscheme
29 * name - either a hex RGB triplet or a named colour under java.awt.color ). The
30 * values of the colourscheme constants is important for callers of
31 * getColourName(int i), since it can be used to enumerate the set of built in
32 * colours. The FIRST_COLOUR and LAST_COLOUR symbols are provided for this.
37 public class ColourSchemeProperty
39 /** Undefined Colourscheme Index */
40 public static final int UNDEFINED = -1;
42 /** for schemes defined on the fly */
43 public static final int USER_DEFINED = 0;
45 /** No Colourscheme Index */
46 public static final int NONE = 1;
49 public static final int CLUSTAL = 2;
52 public static final int BLOSUM = 3;
55 public static final int PID = 4;
58 public static final int ZAPPO = 5;
61 public static final int TAYLOR = 6;
64 public static final int HYDROPHOBIC = 7;
67 public static final int HELIX = 8;
70 public static final int STRAND = 9;
73 public static final int TURN = 10;
76 public static final int BURIED = 11;
79 public static final int NUCLEOTIDE = 12;
84 public static final int PURINEPYRIMIDINE = 13;
86 public static final int COVARIATION = 14;
88 public static final int TCOFFEE = 15;
90 public static final int RNAHELIX = 16;
93 * index of first colourscheme (includes 'None')
95 public static final int FIRST_COLOUR = NONE;
97 public static final int LAST_COLOUR = RNAHELIX;
105 * @return DOCUMENT ME!
107 public static int getColourIndexFromName(String name)
111 if (name.equalsIgnoreCase("Clustal"))
115 else if (name.equalsIgnoreCase("Blosum62"))
119 else if (name.equalsIgnoreCase("% Identity"))
123 else if (name.equalsIgnoreCase("Zappo"))
127 else if (name.equalsIgnoreCase("Taylor"))
131 else if (name.equalsIgnoreCase("Hydrophobic"))
135 else if (name.equalsIgnoreCase("Helix Propensity"))
139 else if (name.equalsIgnoreCase("Strand Propensity"))
143 else if (name.equalsIgnoreCase("Turn Propensity"))
147 else if (name.equalsIgnoreCase("Buried Index"))
151 else if (name.equalsIgnoreCase("Nucleotide"))
155 else if (name.equalsIgnoreCase("T-Coffee Scores"))
160 else if (name.equalsIgnoreCase("User Defined"))
164 else if (name.equalsIgnoreCase("None"))
168 else if (name.equalsIgnoreCase("Purine/Pyrimidine"))
170 ret = PURINEPYRIMIDINE;
172 else if (name.equalsIgnoreCase("RNA Helices"))
176 // else if (name.equalsIgnoreCase("Covariation"))
178 // ret = COVARIATION;
190 * @return DOCUMENT ME!
192 public static String getColourName(ColourSchemeI cs)
197 if (cs instanceof ClustalxColourScheme)
201 else if (cs instanceof Blosum62ColourScheme)
205 else if (cs instanceof PIDColourScheme)
209 else if (cs instanceof ZappoColourScheme)
213 else if (cs instanceof TaylorColourScheme)
217 else if (cs instanceof HydrophobicColourScheme)
221 else if (cs instanceof HelixColourScheme)
225 else if (cs instanceof StrandColourScheme)
229 else if (cs instanceof TurnColourScheme)
233 else if (cs instanceof BuriedColourScheme)
237 else if (cs instanceof NucleotideColourScheme)
241 else if (cs instanceof PurinePyrimidineColourScheme)
243 index = PURINEPYRIMIDINE;
245 else if (cs instanceof TCoffeeColourScheme)
249 else if (cs instanceof RNAHelicesColour)
254 * else if (cs instanceof CovariationColourScheme) { index = COVARIATION; }
256 else if (cs instanceof UserColourScheme)
258 if ((((UserColourScheme) cs).getName() != null)
259 && (((UserColourScheme) cs).getName().length() > 0))
261 return ((UserColourScheme) cs).getName();
263 // get default colourscheme name
264 index = USER_DEFINED;
267 return getColourName(index);
276 * @return DOCUMENT ME!
278 public static String getColourName(int index)
314 ret = "Helix Propensity";
319 ret = "Strand Propensity";
324 ret = "Turn Propensity";
329 ret = "Buried Index";
338 case PURINEPYRIMIDINE:
339 ret = "Purine/Pyrimidine";
344 ret = "T-Coffee Scores";
352 * case COVARIATION: ret = "Covariation";
357 ret = "User Defined";
371 * retrieve or create colourscheme associated with name
374 * sequences to colour
376 * range of sequences to colour
378 * colourscheme name, applet colour parameter specification, or
379 * string to parse as colour for new coloursheme
380 * @return Valid Colourscheme
382 public static ColourSchemeI getColour(AnnotatedCollectionI alignment,
385 int colindex = getColourIndexFromName(name);
386 if (colindex == UNDEFINED)
388 if (name.indexOf('=') == -1)
390 // try to build a colour from the string directly
393 return new UserColourScheme(name);
394 } catch (Exception e)
396 // System.err.println("Ignoring unknown colourscheme name");
401 // try to parse the string as a residue colourscheme
404 // fix the launchApp user defined coloursheme transfer bug
405 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
407 ucs.parseAppletParameter(name);
409 } catch (Exception e)
411 // System.err.println("Ignoring exception when parsing colourscheme as applet-parameter");
415 return getColour(alignment, getColourIndexFromName(name));
419 * Construct an instance of ColourSchemeI corresponding to the given
423 * sequences to be coloured by colourscheme
425 * geometry of alignment
427 * colourscheme number
429 * @return null or an instance of the colourscheme configured to colour given
432 public static ColourSchemeI getColour(
433 jalview.datamodel.AnnotatedCollectionI coll, int index)
435 // TODO 3.0 2.8 refactor signature to take an alignmentI like container so
436 // colourschemes based on annotation can be initialised
437 ColourSchemeI cs = null;
442 cs = new ClustalxColourScheme(coll, null);
447 cs = new Blosum62ColourScheme();
452 cs = new PIDColourScheme();
457 cs = new ZappoColourScheme();
462 cs = new TaylorColourScheme();
466 cs = new HydrophobicColourScheme();
471 cs = new HelixColourScheme();
476 cs = new StrandColourScheme();
481 cs = new TurnColourScheme();
486 cs = new BuriedColourScheme();
491 cs = new NucleotideColourScheme();
495 case PURINEPYRIMIDINE:
496 cs = new PurinePyrimidineColourScheme();
501 cs = new TCoffeeColourScheme(coll);
505 cs = new RNAHelicesColour(coll);
509 // cs = new CovariationColourScheme(annotation);
514 Color[] col = new Color[24];
515 for (int i = 0; i < 24; i++)
517 col[i] = Color.white;
519 cs = new UserColourScheme(col);
529 public static Color getAWTColorFromName(String name)
532 name = name.toLowerCase();
533 if (name.equals("black"))
537 else if (name.equals("blue"))
541 else if (name.equals("cyan"))
545 else if (name.equals("darkGray"))
547 col = Color.darkGray;
549 else if (name.equals("gray"))
553 else if (name.equals("green"))
557 else if (name.equals("lightGray"))
559 col = Color.lightGray;
561 else if (name.equals("magenta"))
565 else if (name.equals("orange"))
569 else if (name.equals("pink"))
573 else if (name.equals("red"))
577 else if (name.equals("white"))
581 else if (name.equals("yellow"))