X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=98e90bdf769f07363b4b8bb598d97a5edf6d3db2;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=84b660fe7fad68f57426394f36e3e8dcced41017;hpb=7377fb763b212300084f293fcfb6789eb5e49ff3;p=jalview.git diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java index 84b660f..98e90bd 100755 --- a/src/jalview/schemes/ColourSchemeProperty.java +++ b/src/jalview/schemes/ColourSchemeProperty.java @@ -1,24 +1,28 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) - * Copyright (C) 2014 The Jalview Authors + * 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. + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. * * 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 Jalview. If not, see . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.schemes; +import jalview.api.AlignViewportI; import jalview.datamodel.AnnotatedCollectionI; +import jalview.util.ColorUtils; import java.awt.Color; @@ -36,566 +40,117 @@ import java.awt.Color; */ public class ColourSchemeProperty { - /** Undefined Colourscheme Index */ - public static final int UNDEFINED = -1; - - /** for schemes defined on the fly */ - public static final int USER_DEFINED = 0; - - /** No Colourscheme Index */ - public static final int NONE = 1; - - /** DOCUMENT ME!! */ - public static final int CLUSTAL = 2; - - /** DOCUMENT ME!! */ - public static final int BLOSUM = 3; - - /** DOCUMENT ME!! */ - public static final int PID = 4; - - /** DOCUMENT ME!! */ - public static final int ZAPPO = 5; - - /** DOCUMENT ME!! */ - public static final int TAYLOR = 6; - - /** DOCUMENT ME!! */ - public static final int HYDROPHOBIC = 7; - - /** DOCUMENT ME!! */ - public static final int HELIX = 8; - - /** DOCUMENT ME!! */ - public static final int STRAND = 9; - - /** DOCUMENT ME!! */ - public static final int TURN = 10; - - /** DOCUMENT ME!! */ - public static final int BURIED = 11; - - /** DOCUMENT ME!! */ - public static final int NUCLEOTIDE = 12; /** - * purine/pyrimidine - */ - public static final int PURINEPYRIMIDINE = 13; - - public static final int COVARIATION = 14; - - public static final int TCOFFEE = 15; - - public static final int RNAHELIX = 16; - - public static final int RNAINTERACTION = 16; - - /** - * index of first colourscheme (includes 'None') - */ - public static final int FIRST_COLOUR = NONE; - - public static final int LAST_COLOUR = RNAHELIX; - - /** - * 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(AlignViewportI view, + 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("T-Coffee Scores")) - { - ret = TCOFFEE; - } + return null; - else if (name.equalsIgnoreCase("User Defined")) - { - ret = USER_DEFINED; - } - else if (name.equalsIgnoreCase("None")) - { - ret = NONE; - } - else if (name.equalsIgnoreCase("Purine/Pyrimidine")) - { - ret = PURINEPYRIMIDINE; } - else if (name.equalsIgnoreCase("RNA Interaction type")) - { - ret = RNAINTERACTION; - } - else if (name.equalsIgnoreCase("RNA Helices")) + + /* + * if this is the name of a registered colour scheme, just + * create a new instance of it + */ + ColourSchemeI scheme = ColourSchemes.getInstance().getColourScheme(name, + view, forData, null); + if (scheme != null) { - ret = RNAHELIX; + return scheme; } - // else if (name.equalsIgnoreCase("Covariation")) - // { - // ret = COVARIATION; - // } - 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) - { - - int index = NONE; + public static Color rnaHelices[] = null; - 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) - { - index = BURIED; - } - else if (cs instanceof NucleotideColourScheme) - { - index = NUCLEOTIDE; - } - else if (cs instanceof PurinePyrimidineColourScheme) + public static void initRnaHelicesShading(int n) + { + int j = 0; + if (rnaHelices == null) { - index = PURINEPYRIMIDINE; + rnaHelices = new Color[n + 1]; } - else if (cs instanceof TCoffeeColourScheme) + else if (rnaHelices != null && rnaHelices.length <= n) { - index = TCOFFEE; + Color[] t = new Color[n + 1]; + System.arraycopy(rnaHelices, 0, t, 0, rnaHelices.length); + j = rnaHelices.length; + rnaHelices = t; } - else if (cs instanceof RNAHelicesColour) + else { - index = RNAHELIX; + return; } - /* - * else if (cs instanceof CovariationColourScheme) { index = COVARIATION; } - */ - else if (cs instanceof UserColourScheme) + // Generate random colors and store + for (; j <= n; j++) { - if ((((UserColourScheme) cs).getName() != null) - && (((UserColourScheme) cs).getName().length() > 0)) - { - return ((UserColourScheme) cs).getName(); - } - // get default colourscheme name - index = USER_DEFINED; + rnaHelices[j] = ColorUtils.generateRandomColor(Color.white); } - - return getColourName(index); } /** - * DOCUMENT ME! - * - * @param index - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * delete the existing cached RNA helices colours */ - public static String getColourName(int index) + public static void resetRnaHelicesShading() { - String ret = null; - - switch (index) - { - 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 PURINEPYRIMIDINE: - ret = "Purine/Pyrimidine"; - - break; - - case TCOFFEE: - ret = "T-Coffee Scores"; - - break; -<<<<<<< HEAD - - case RNAINTERACTION: - ret = "RNA Interaction type"; - - break; -======= - case RNAHELIX: - ret = "RNA Helices"; - - break; ->>>>>>> JAL-952_rnahelix - /* - * case COVARIATION: ret = "Covariation"; - * - * break; - */ - case USER_DEFINED: - ret = "User Defined"; - - break; - - default: - ret = "None"; - - break; - } - - return ret; + rnaHelices = null; } /** - * retrieve or create colourscheme associated with name + * Returns the name of the colour scheme (or "None" if it is null) * - * @param seqs - * sequences to colour - * @param width - * range of sequences to colour - * @param name - * colourscheme name, applet colour parameter specification, or - * string to parse as colour for new coloursheme - * @return Valid Colourscheme + * @param cs + * @return */ - public static ColourSchemeI getColour(AnnotatedCollectionI alignment, - String name) + public static String getColourName(ColourSchemeI cs) { - int colindex = getColourIndexFromName(name); - if (colindex == UNDEFINED) - { - if (name.indexOf('=') == -1) - { - // try to build a colour from the string directly - try - { - return new UserColourScheme(name); - } catch (Exception e) - { - // System.err.println("Ignoring unknown colourscheme name"); - } - } - else - { - // try to parse the string as a residue colourscheme - try - { - // fix the launchApp user defined coloursheme transfer bug - jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme( - "white"); - ucs.parseAppletParameter(name); - - } catch (Exception e) - { - // System.err.println("Ignoring exception when parsing colourscheme as applet-parameter"); - } - } - } - return getColour(alignment, getColourIndexFromName(name)); + return cs == null ? ResidueColourScheme.NONE : cs.getSchemeName(); } - /** - * Construct an instance of ColourSchemeI corresponding to the given - * colourscheme index - * - * @param seqs - * sequences to be coloured by colourscheme - * @param width - * geometry of alignment - * @param index - * colourscheme number - * - * @return null or an instance of the colourscheme configured to colour given - * sequence set - */ - public static ColourSchemeI getColour( - jalview.datamodel.AnnotatedCollectionI coll, int index) - { - // TODO 3.0 2.8 refactor signature to take an alignmentI like container so - // colourschemes based on annotation can be initialised - ColourSchemeI cs = null; - - switch (index) - { - case CLUSTAL: - cs = new ClustalxColourScheme(coll, null); - - 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 PURINEPYRIMIDINE: - cs = new PurinePyrimidineColourScheme(); - - break; - - case TCOFFEE: - cs = new TCoffeeColourScheme(coll); - break; - - case RNAHELIX: - cs = new RNAHelicesColour(coll); - break; - - // case COVARIATION: - // cs = new CovariationColourScheme(annotation); - // 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; - } }