X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=98e90bdf769f07363b4b8bb598d97a5edf6d3db2;hb=b9b1f47cc74bbec8c28b75776e1d00c258215dfb;hp=169f35ef114640c7acea32dbb2e6e84b1895d453;hpb=6ab383a26fe6e42b6a5dca4b2132322c660a4c37;p=jalview.git diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java index 169f35e..98e90bd 100755 --- a/src/jalview/schemes/ColourSchemeProperty.java +++ b/src/jalview/schemes/ColourSchemeProperty.java @@ -1,77 +1,156 @@ +/* + * 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. + * + * 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.api.AlignViewportI; +import jalview.datamodel.AnnotatedCollectionI; +import jalview.util.ColorUtils; + +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 { - public static final int CLUSTAL = 0; - public static final int BLOSUM = 1; - public static final int PID = 2; - public static final int ZAPPO = 3; - public static final int HYDROPHOBIC=4; - public static final int HELIX=5; - public static final int STRAND=6; - public static final int TURN = 7; - public static final int BURIED = 8; - public static final int NUCLEOTIDE = 9; - public static final int USER_DEFINED = 10; - public static final int NONE = 11; - - public static String getColourName(int index) + /** + * 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 + * + * + * If none of these formats is matched, the string is converted to a colour + * using a hashing algorithm. For name "None", returns null. + * + * @param forData + * @param name + * @return + */ + public static ColourSchemeI getColourScheme(AlignViewportI view, + AnnotatedCollectionI forData, String name) { - String ret=null; - switch(index) + if (ResidueColourScheme.NONE.equalsIgnoreCase(name)) { - 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 null; + } - return ret; - } - public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, String name) - { - for(int i=0; i<12; i++) + /* + * 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) { - if(getColourName(i).equals(name)) - return getColour(al, i); + return scheme; } - return null; + + /* + * 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; } - public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, int index) + public static Color rnaHelices[] = null; + + public static void initRnaHelicesShading(int n) { - ColourSchemeI cs = null; - switch(index) + int j = 0; + if (rnaHelices == null) { - case CLUSTAL: cs = new ClustalxColourScheme(al.getSequences(), al.getWidth()); 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: - if(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR")!=null) - { - cs = jalview.gui.UserDefinedColours.loadDefaultColours(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR")); - } - break; - - default: break; + 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] = ColorUtils.generateRandomColor(Color.white); + } + } - return cs; + /** + * delete the existing cached RNA helices colours + */ + public static void resetRnaHelicesShading() + { + rnaHelices = null; } + + /** + * Returns the name of the colour scheme (or "None" if it is null) + * + * @param cs + * @return + */ + public static String getColourName(ColourSchemeI cs) + { + return cs == null ? ResidueColourScheme.NONE : cs.getSchemeName(); + } + }