X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=a7f23110d43185c94c421c0b509c3a5534efa438;hb=dbddb1d9b57c2bd3a70b5930fcb69eb6fce22878;hp=ef2feac1effb489b9fefd76c07ccdf8dfd40d786;hpb=681588b5dfb7e3ff34ceaccdf47f2dae6bd590ce;p=jalview.git diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java index ef2feac..a7f2311 100755 --- a/src/jalview/schemes/ColourSchemeProperty.java +++ b/src/jalview/schemes/ColourSchemeProperty.java @@ -1,86 +1,108 @@ /* - * 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 - * 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 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * + * 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 . */ package jalview.schemes; -import java.awt.*; +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 ) + * 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; + /** Undefined Colourscheme Index */ + public static final int UNDEFINED = -1; - /** DOCUMENT ME!! */ - public static final int BLOSUM = 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 PID = 2; + public static final int CLUSTAL = 2; /** DOCUMENT ME!! */ - public static final int ZAPPO = 3; + public static final int BLOSUM = 3; /** DOCUMENT ME!! */ - public static final int TAYLOR = 4; + public static final int PID = 4; /** DOCUMENT ME!! */ - public static final int HYDROPHOBIC = 5; + public static final int ZAPPO = 5; /** DOCUMENT ME!! */ - public static final int HELIX = 6; + public static final int TAYLOR = 6; /** DOCUMENT ME!! */ - public static final int STRAND = 7; + public static final int HYDROPHOBIC = 7; /** DOCUMENT ME!! */ - public static final int TURN = 8; + public static final int HELIX = 8; /** DOCUMENT ME!! */ - public static final int BURIED = 9; + public static final int STRAND = 9; /** DOCUMENT ME!! */ - public static final int NUCLEOTIDE = 10; + public static final int TURN = 10; /** DOCUMENT ME!! */ - public static final int USER_DEFINED = 11; + public static final int BURIED = 11; /** DOCUMENT ME!! */ - public static final int NONE = 12; + 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; + + + /** + * index of first colourscheme (includes 'None') + */ + public static final int FIRST_COLOUR = NONE; + + public static final int LAST_COLOUR = NUCLEOTIDE; /** * DOCUMENT ME! * * @param name - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ public static int getColourIndexFromName(String name) { - int ret = 12; + int ret = UNDEFINED; if (name.equalsIgnoreCase("Clustal")) { @@ -126,10 +148,19 @@ public class ColourSchemeProperty { 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; + } return ret; } @@ -138,14 +169,14 @@ public class ColourSchemeProperty * DOCUMENT ME! * * @param cs - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ public static String getColourName(ColourSchemeI cs) { - int index = 12; + int index = NONE; if (cs instanceof ClustalxColourScheme) { @@ -209,7 +240,7 @@ public class ColourSchemeProperty * DOCUMENT ME! * * @param index - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -291,9 +322,9 @@ public class ColourSchemeProperty * DOCUMENT ME! * * @param al - * DOCUMENT ME! + * DOCUMENT ME! * @param name - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -304,49 +335,69 @@ public class ColourSchemeProperty } /** - * DOCUMENT ME! + * retrieve or create colourscheme associated with name * * @param seqs - * DOCUMENT ME! + * sequences to colour * @param width - * DOCUMENT ME! + * range of sequences to colour * @param name - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * colourscheme name, applet colour parameter specification, or + * string to parse as colour for new coloursheme + * @return Valid Colourscheme */ public static ColourSchemeI getColour(java.util.Vector seqs, int width, String name) { int colindex = getColourIndexFromName(name); - if (colindex > USER_DEFINED) + if (colindex == UNDEFINED) { - try + if (name.indexOf('=') == -1) { - return new UserColourScheme(name); - } catch (Exception e) + // 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 { - // System.err.println("Ignoring unknown colourscheme name"); + // 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(seqs, width, getColourIndexFromName(name)); } /** - * DOCUMENT ME! + * Construct an instance of ColourSchemeI corresponding to the given colourscheme index * * @param seqs - * DOCUMENT ME! + * sequences to be coloured by colourscheme * @param width - * DOCUMENT ME! + * geometry of alignment * @param index - * DOCUMENT ME! + * colourscheme number * - * @return DOCUMENT ME! + * @return null or an instance of the colourscheme configured to colour given sequence set */ public static ColourSchemeI getColour(java.util.Vector seqs, int width, 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)