X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=500047b1e554a1423a4a6cfaf04872716aa8bb8d;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=d27dcf012972f2a43fd081f4a29e20748803ec61;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java index d27dcf0..500047b 100755 --- a/src/jalview/schemes/ColourSchemeProperty.java +++ b/src/jalview/schemes/ColourSchemeProperty.java @@ -1,406 +1,637 @@ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 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 -* 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. -* -* 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 -*/ -package jalview.schemes; - -import java.awt.*; -/** - * DOCUMENT ME! - * - * @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 HYDROPHOBIC = 4; - - /** DOCUMENT ME!! */ - public static final int HELIX = 5; - - /** DOCUMENT ME!! */ - public static final int STRAND = 6; - - /** DOCUMENT ME!! */ - public static final int TURN = 7; - - /** DOCUMENT ME!! */ - public static final int BURIED = 8; - - /** DOCUMENT ME!! */ - public static final int NUCLEOTIDE = 9; - - /** DOCUMENT ME!! */ - public static final int USER_DEFINED = 10; - - /** DOCUMENT ME!! */ - public static final int NONE = 11; - - /** - * DOCUMENT ME! - * - * @param name DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public static int getColourIndexFromName(String name) - { - int ret = 11; - - if (name.equalsIgnoreCase("Clustal")) - { - 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("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 ret; - } - - /** - * DOCUMENT ME! - * - * @param cs DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public static String getColourName(ColourSchemeI cs) - { - if (cs instanceof ConservationColourScheme) - { - cs = ((ConservationColourScheme) cs).cs; - } - - int index = 11; - - 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 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 UserColourScheme) - { - index = USER_DEFINED; - } - - return getColourName(index); - } - - /** - * DOCUMENT ME! - * - * @param index DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public static String getColourName(int index) - { - 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 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; - } - - return ret; - } - - /** - * DOCUMENT ME! - * - * @param al DOCUMENT ME! - * @param name DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, - String name) - { - return getColour(al.getSequences(), al.getWidth(), name); - } - - /** - * DOCUMENT ME! - * - * @param seqs DOCUMENT ME! - * @param width DOCUMENT ME! - * @param name DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public static ColourSchemeI getColour(java.util.Vector seqs, int width, - String name) - { - return getColour(seqs, width, getColourIndexFromName(name)); - } - - /** - * 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 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: - cs = new UserColourScheme(new Color[0]); - - 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; - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 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. + * + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.schemes; + +import jalview.datamodel.AnnotatedCollectionI; + +import java.awt.Color; + +/** + * 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 ). 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 +{ + /** 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 = 17; + + /** + * index of first colourscheme (includes 'None') + */ + public static final int FIRST_COLOUR = NONE; + + public static final int LAST_COLOUR = RNAINTERACTION; + + /** + * DOCUMENT ME! + * + * @param name + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public static int getColourIndexFromName(String name) + { + int ret = UNDEFINED; + + if (name.equalsIgnoreCase("Clustal")) + { + 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; + } + + 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")) + { + ret = RNAHELIX; + } + // else if (name.equalsIgnoreCase("Covariation")) + // { + // ret = COVARIATION; + // } + + return ret; + } + + /** + * DOCUMENT ME! + * + * @param cs + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public static String getColourName(ColourSchemeI cs) + { + + 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) + { + index = BURIED; + } + else if (cs instanceof NucleotideColourScheme) + { + index = NUCLEOTIDE; + } + else if (cs instanceof PurinePyrimidineColourScheme) + { + index = PURINEPYRIMIDINE; + } + else if (cs instanceof TCoffeeColourScheme) + { + index = TCOFFEE; + } + else if (cs instanceof RNAHelicesColour) + { + index = RNAHELIX; + } + /* + * else if (cs instanceof CovariationColourScheme) { index = COVARIATION; } + */ + else if (cs instanceof UserColourScheme) + { + if ((((UserColourScheme) cs).getName() != null) + && (((UserColourScheme) cs).getName().length() > 0)) + { + return ((UserColourScheme) cs).getName(); + } + // get default colourscheme name + index = USER_DEFINED; + } + + return getColourName(index); + } + + /** + * DOCUMENT ME! + * + * @param index + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public static String getColourName(int index) + { + 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; + + case RNAINTERACTION: + ret = "RNA Interaction type"; + + break; + case RNAHELIX: + ret = "RNA Helices"; + + break; + /* + * case COVARIATION: ret = "Covariation"; + * + * break; + */ + case USER_DEFINED: + ret = "User Defined"; + + break; + + default: + ret = "None"; + + break; + } + + return ret; + } + + /** + * retrieve or create colourscheme associated with name + * + * @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 + */ + public static ColourSchemeI getColour(AnnotatedCollectionI alignment, + String name) + { + 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)); + } + + /** + * 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; + } + + public static Color rnaHelices[] = null; + + public static void initRnaHelicesShading(int n) + { + int j = 0; + if (rnaHelices == null) + { + rnaHelices = new Color[n + 1]; + } + else if (rnaHelices != null && rnaHelices.length <= n) + { + Color[] t = new Color[n + 1]; + System.arraycopy(rnaHelices, 0, t, 0, rnaHelices.length); + j = rnaHelices.length; + rnaHelices = t; + } + else + { + return; + } + // Generate random colors and store + for (; j <= n; j++) + { + rnaHelices[j] = jalview.util.ColorUtils + .generateRandomColor(Color.white); + } + } + + /** + * delete the existing cached RNA helces colours + */ + public static void resetRnaHelicesShading() + { + rnaHelices = null; + } + +}