X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=1e2db769d4f445c30b54505380e9737678e5315c;hb=a7f8fa9c06d82efbbdbc6a0bf1054bb21610b353;hp=4519f91db76df7657205c1c4677e428c300535c8;hpb=bd248212fee44557d973432f42666780530db8ed;p=jalview.git diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java index 4519f91..1e2db76 100755 --- a/src/jalview/schemes/ColourSchemeProperty.java +++ b/src/jalview/schemes/ColourSchemeProperty.java @@ -1,33 +1,35 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 + * 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 + * + * 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 jalview.datamodel.AnnotatedCollectionI; + +import java.awt.Color; /** - * ColourSchemeProperty Binds names to hardwired colourschemes and tries to deal + * 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 $Revision$ */ @@ -82,6 +84,9 @@ public class ColourSchemeProperty public static final int COVARIATION = 14; + public static final int TCOFFEE = 15; + + /** * index of first colourscheme (includes 'None') */ @@ -91,10 +96,10 @@ public class ColourSchemeProperty /** * DOCUMENT ME! - * + * * @param name * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public static int getColourIndexFromName(String name) @@ -145,6 +150,11 @@ public class ColourSchemeProperty { ret = NUCLEOTIDE; } + else if (name.equalsIgnoreCase("T-Coffee Scores")) + { + ret = TCOFFEE; + } + else if (name.equalsIgnoreCase("User Defined")) { ret = USER_DEFINED; @@ -153,16 +163,24 @@ public class ColourSchemeProperty { ret = NONE; } + else if (name.equalsIgnoreCase("Purine/Pyrimidine")) + { + ret = PURINEPYRIMIDINE; + } + // else if (name.equalsIgnoreCase("Covariation")) + // { + // ret = COVARIATION; + // } return ret; } /** * DOCUMENT ME! - * + * * @param cs * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public static String getColourName(ColourSchemeI cs) @@ -214,6 +232,17 @@ public class ColourSchemeProperty { index = NUCLEOTIDE; } + else if (cs instanceof PurinePyrimidineColourScheme) + { + index = PURINEPYRIMIDINE; + } + else if (cs instanceof TCoffeeColourScheme) + { + index = TCOFFEE; + } + /* + * else if (cs instanceof CovariationColourScheme) { index = COVARIATION; } + */ else if (cs instanceof UserColourScheme) { if ((((UserColourScheme) cs).getName() != null) @@ -230,10 +259,10 @@ public class ColourSchemeProperty /** * DOCUMENT ME! - * + * * @param index * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public static String getColourName(int index) @@ -296,6 +325,20 @@ public class ColourSchemeProperty break; + case PURINEPYRIMIDINE: + ret = "Purine/Pyrimidine"; + + break; + + case TCOFFEE: + ret = "T-Coffee Scores"; + + break; + /* + * case COVARIATION: ret = "Covariation"; + * + * break; + */ case USER_DEFINED: ret = "User Defined"; @@ -309,26 +352,9 @@ public class ColourSchemeProperty 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); - } - /** * retrieve or create colourscheme associated with name - * + * * @param seqs * sequences to colour * @param width @@ -338,7 +364,7 @@ public class ColourSchemeProperty * string to parse as colour for new coloursheme * @return Valid Colourscheme */ - public static ColourSchemeI getColour(java.util.Vector seqs, int width, + public static ColourSchemeI getColour(AnnotatedCollectionI alignment, String name) { int colindex = getColourIndexFromName(name); @@ -371,30 +397,30 @@ public class ColourSchemeProperty } } } - return getColour(seqs, width, getColourIndexFromName(name)); + return getColour(alignment, 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! - * - * @return DOCUMENT ME! + * colourscheme number + * + * @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) + 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(seqs, width); + cs = new ClustalxColourScheme(coll, null); break; @@ -447,6 +473,18 @@ public class ColourSchemeProperty break; + case PURINEPYRIMIDINE: + cs = new PurinePyrimidineColourScheme(); + + break; + + case TCOFFEE: + cs = new TCoffeeColourScheme(coll); + // case COVARIATION: + // cs = new CovariationColourScheme(annotation); + + // break; + case USER_DEFINED: Color[] col = new Color[24]; for (int i = 0; i < 24; i++)