X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=a7f23110d43185c94c421c0b509c3a5534efa438;hb=dbddb1d9b57c2bd3a70b5930fcb69eb6fce22878;hp=dd4eb53f4b68312b277ec30f4fb9d96843ca07f5;hpb=fddbe4cfde483f487a99b30f4a44100112995193;p=jalview.git diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java index dd4eb53..a7f2311 100755 --- a/src/jalview/schemes/ColourSchemeProperty.java +++ b/src/jalview/schemes/ColourSchemeProperty.java @@ -1,77 +1,96 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, 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 file is part of Jalview. * - * 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 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. * - * 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 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; + + /** 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 BLOSUM = 1; + public static final int CLUSTAL = 2; /** DOCUMENT ME!! */ - public static final int PID = 2; + public static final int BLOSUM = 3; /** DOCUMENT ME!! */ - public static final int ZAPPO = 3; + public static final int PID = 4; /** DOCUMENT ME!! */ - public static final int TAYLOR = 4; + public static final int ZAPPO = 5; /** DOCUMENT ME!! */ - public static final int HYDROPHOBIC = 5; + public static final int TAYLOR = 6; /** DOCUMENT ME!! */ - public static final int HELIX = 6; + public static final int HYDROPHOBIC = 7; /** DOCUMENT ME!! */ - public static final int STRAND = 7; + public static final int HELIX = 8; /** DOCUMENT ME!! */ - public static final int TURN = 8; + public static final int STRAND = 9; /** DOCUMENT ME!! */ - public static final int BURIED = 9; + public static final int TURN = 10; /** DOCUMENT ME!! */ - public static final int NUCLEOTIDE = 10; + public static final int BURIED = 11; /** DOCUMENT ME!! */ - public static final int USER_DEFINED = 11; + public static final int NUCLEOTIDE = 12; - /** No Colourscheme Index */ - public static final int NONE = 12; + /** + * purine/pyrimidine + */ + public static final int PURINEPYRIMIDINE = 13; - /** Undefined Colourscheme Index */ - public static final int UNDEFINED = 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! @@ -129,6 +148,11 @@ public class ColourSchemeProperty { ret = NUCLEOTIDE; } + else if (name.equalsIgnoreCase("T-Coffee scores")) + { + ret = TCOFFEE; + } + else if (name.equalsIgnoreCase("User Defined")) { ret = USER_DEFINED; @@ -359,20 +383,21 @@ public class ColourSchemeProperty } /** - * 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)