X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=fc92cd96b2f400fcb0cc4739d640f6b28df25877;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=2f81d13826c5b10da107695f287293765caddf45;hpb=7b999e54e654437cdd7d341bded0be02c10fc917;p=jalview.git diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java index 2f81d13..fc92cd9 100755 --- a/src/jalview/schemes/ColourSchemeProperty.java +++ b/src/jalview/schemes/ColourSchemeProperty.java @@ -1,490 +1,155 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program 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 2 + * 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. - * - * This program 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. - * + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.schemes; -import java.awt.*; +import jalview.datamodel.AnnotatedCollectionI; +import jalview.util.ColorUtils; + +import java.awt.Color; /** - * ColourSchemeProperty Binds names to hardwired colourschemes and tries to deal + * ColourSchemeProperty binds names to hardwired colourschemes and tries to deal * intelligently with mapping unknown names to user defined colourschemes (that * exist or can be created from the string representation of the colourscheme - * name - either a hex RGB triplet or a named colour under java.awt.color ) + * name - either a hex RGB triplet or a named colour under java.awt.color ). The + * values of the colourscheme constants is important for callers of + * getColourName(int i), since it can be used to enumerate the set of built in + * colours. The FIRST_COLOUR and LAST_COLOUR symbols are provided for this. * * @author $author$ * @version $Revision$ */ public class ColourSchemeProperty { - /** DOCUMENT ME!! */ - public static final int CLUSTAL = 0; - - /** DOCUMENT ME!! */ - public static final int BLOSUM = 1; - - /** DOCUMENT ME!! */ - public static final int PID = 2; - - /** DOCUMENT ME!! */ - public static final int ZAPPO = 3; - - /** DOCUMENT ME!! */ - public static final int TAYLOR = 4; - - /** DOCUMENT ME!! */ - public static final int HYDROPHOBIC = 5; - - /** DOCUMENT ME!! */ - public static final int HELIX = 6; - - /** DOCUMENT ME!! */ - public static final int STRAND = 7; - - /** DOCUMENT ME!! */ - public static final int TURN = 8; - - /** DOCUMENT ME!! */ - public static final int BURIED = 9; - - /** DOCUMENT ME!! */ - public static final int NUCLEOTIDE = 10; - - /** DOCUMENT ME!! */ - public static final int USER_DEFINED = 11; - - /** No Colourscheme Index */ - public static final int NONE = 12; - /** Undefined Colourscheme Index */ - public static final int UNDEFINED = 13; - /** - * DOCUMENT ME! + * Returns a colour scheme for the given name, with which the given data may + * be coloured. The name is not case-sensitive, and may be one of + * * - * @param name - * DOCUMENT ME! + * If none of these formats is matched, the string is converted to a colour + * using a hashing algorithm. For name "None", returns null. * - * @return DOCUMENT ME! + * @param forData + * @param name + * @return */ - public static int getColourIndexFromName(String name) + public static ColourSchemeI getColourScheme(AnnotatedCollectionI forData, + String name) { - int ret = UNDEFINED; - - if (name.equalsIgnoreCase("Clustal")) + if (ResidueColourScheme.NONE.equalsIgnoreCase(name)) { - ret = CLUSTAL; - } - else if (name.equalsIgnoreCase("Blosum62")) - { - ret = BLOSUM; - } - else if (name.equalsIgnoreCase("% Identity")) - { - ret = PID; - } - else if (name.equalsIgnoreCase("Zappo")) - { - ret = ZAPPO; - } - else if (name.equalsIgnoreCase("Taylor")) - { - ret = TAYLOR; - } - else if (name.equalsIgnoreCase("Hydrophobic")) - { - ret = HYDROPHOBIC; - } - else if (name.equalsIgnoreCase("Helix Propensity")) - { - ret = HELIX; - } - else if (name.equalsIgnoreCase("Strand Propensity")) - { - ret = STRAND; - } - else if (name.equalsIgnoreCase("Turn Propensity")) - { - ret = TURN; - } - else if (name.equalsIgnoreCase("Buried Index")) - { - ret = BURIED; - } - else if (name.equalsIgnoreCase("Nucleotide")) - { - ret = NUCLEOTIDE; - } - else if (name.equalsIgnoreCase("User Defined")) - { - ret = USER_DEFINED; + return null; + } - else if (name.equalsIgnoreCase("None")) + + /* + * if this is the name of a registered colour scheme, just + * create a new instance of it + */ + ColourSchemeI scheme = ColourSchemes.getInstance().getColourScheme(name, + forData, null); + if (scheme != null) { - ret = NONE; + return scheme; } - return ret; + /* + * try to parse the string as a residues colour scheme + * e.g. A=red;T,G=blue etc + * else parse the name as a colour specification + * e.g. "red" or "ff00ed", + * or failing that hash the name to a colour + */ + UserColourScheme ucs = new UserColourScheme(name); + return ucs; } - /** - * DOCUMENT ME! - * - * @param cs - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public static String getColourName(ColourSchemeI cs) - { + public static Color rnaHelices[] = null; - int index = NONE; - - if (cs instanceof ClustalxColourScheme) - { - index = CLUSTAL; - } - else if (cs instanceof Blosum62ColourScheme) - { - index = BLOSUM; - } - else if (cs instanceof PIDColourScheme) - { - index = PID; - } - else if (cs instanceof ZappoColourScheme) - { - index = ZAPPO; - } - else if (cs instanceof TaylorColourScheme) - { - index = TAYLOR; - } - else if (cs instanceof HydrophobicColourScheme) - { - index = HYDROPHOBIC; - } - else if (cs instanceof HelixColourScheme) - { - index = HELIX; - } - else if (cs instanceof StrandColourScheme) - { - index = STRAND; - } - else if (cs instanceof TurnColourScheme) - { - index = TURN; - } - else if (cs instanceof BuriedColourScheme) + public static void initRnaHelicesShading(int n) + { + int j = 0; + if (rnaHelices == null) { - index = BURIED; + rnaHelices = new Color[n + 1]; } - else if (cs instanceof NucleotideColourScheme) + else if (rnaHelices != null && rnaHelices.length <= n) { - index = NUCLEOTIDE; + Color[] t = new Color[n + 1]; + System.arraycopy(rnaHelices, 0, t, 0, rnaHelices.length); + j = rnaHelices.length; + rnaHelices = t; } - else if (cs instanceof UserColourScheme) + else { - if ((((UserColourScheme) cs).getName() != null) - && (((UserColourScheme) cs).getName().length() > 0)) - { - return ((UserColourScheme) cs).getName(); - } - // get default colourscheme name - index = USER_DEFINED; + return; } - - return getColourName(index); - } - - /** - * DOCUMENT ME! - * - * @param index - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public static String getColourName(int index) - { - String ret = null; - - switch (index) + // Generate random colors and store + for (; j <= n; j++) { - case CLUSTAL: - ret = "Clustal"; - - break; - - case BLOSUM: - ret = "Blosum62"; - - break; - - case PID: - ret = "% Identity"; - - break; - - case ZAPPO: - ret = "Zappo"; - - break; - - case TAYLOR: - ret = "Taylor"; - break; - - case HYDROPHOBIC: - ret = "Hydrophobic"; - - break; - - case HELIX: - ret = "Helix Propensity"; - - break; - - case STRAND: - ret = "Strand Propensity"; - - break; - - case TURN: - ret = "Turn Propensity"; - - break; - - case BURIED: - ret = "Buried Index"; - - break; - - case NUCLEOTIDE: - ret = "Nucleotide"; - - break; - - case USER_DEFINED: - ret = "User Defined"; - - break; - - default: - ret = "None"; - - break; + rnaHelices[j] = ColorUtils.generateRandomColor(Color.white); } - - return ret; } /** - * DOCUMENT ME! - * - * @param al - * DOCUMENT ME! - * @param name - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * delete the existing cached RNA helices colours */ - public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, - String name) + public static void resetRnaHelicesShading() { - return getColour(al.getSequences(), al.getWidth(), name); + rnaHelices = null; } /** - * DOCUMENT ME! + * Returns the name of the colour scheme (or "None" if it is null) * - * @param seqs - * DOCUMENT ME! - * @param width - * DOCUMENT ME! - * @param name - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * @param cs + * @return */ - public static ColourSchemeI getColour(java.util.Vector seqs, int width, - String name) + public static String getColourName(ColourSchemeI cs) { - int colindex = getColourIndexFromName(name); - if (colindex == UNDEFINED) // USER_DEFINED) - { - try - { - return new UserColourScheme(name); - } catch (Exception e) - { - // System.err.println("Ignoring unknown colourscheme name"); - } - } - return getColour(seqs, width, getColourIndexFromName(name)); + return cs == null ? ResidueColourScheme.NONE : cs.getSchemeName(); } - /** - * DOCUMENT ME! - * - * @param seqs - * DOCUMENT ME! - * @param width - * DOCUMENT ME! - * @param index - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public static ColourSchemeI getColour(java.util.Vector seqs, int width, - int index) - { - ColourSchemeI cs = null; - - switch (index) - { - case CLUSTAL: - cs = new ClustalxColourScheme(seqs, width); - - break; - - case BLOSUM: - cs = new Blosum62ColourScheme(); - - break; - - case PID: - cs = new PIDColourScheme(); - - break; - - case ZAPPO: - cs = new ZappoColourScheme(); - - break; - - case TAYLOR: - cs = new TaylorColourScheme(); - break; - - case HYDROPHOBIC: - cs = new HydrophobicColourScheme(); - - break; - - case HELIX: - cs = new HelixColourScheme(); - - break; - - case STRAND: - cs = new StrandColourScheme(); - - break; - - case TURN: - cs = new TurnColourScheme(); - - break; - - case BURIED: - cs = new BuriedColourScheme(); - - break; - - case NUCLEOTIDE: - cs = new NucleotideColourScheme(); - - break; - - case USER_DEFINED: - Color[] col = new Color[24]; - for (int i = 0; i < 24; i++) - { - col[i] = Color.white; - } - cs = new UserColourScheme(col); - break; - - default: - break; - } - - return cs; - } - - public static Color getAWTColorFromName(String name) - { - Color col = null; - name = name.toLowerCase(); - if (name.equals("black")) - { - col = Color.black; - } - else if (name.equals("blue")) - { - col = Color.blue; - } - else if (name.equals("cyan")) - { - col = Color.cyan; - } - else if (name.equals("darkGray")) - { - col = Color.darkGray; - } - else if (name.equals("gray")) - { - col = Color.gray; - } - else if (name.equals("green")) - { - col = Color.green; - } - else if (name.equals("lightGray")) - { - col = Color.lightGray; - } - else if (name.equals("magenta")) - { - col = Color.magenta; - } - else if (name.equals("orange")) - { - col = Color.orange; - } - else if (name.equals("pink")) - { - col = Color.pink; - } - else if (name.equals("red")) - { - col = Color.red; - } - else if (name.equals("white")) - { - col = Color.white; - } - else if (name.equals("yellow")) - { - col = Color.yellow; - } - - return col; - } }