X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=500047b1e554a1423a4a6cfaf04872716aa8bb8d;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=2f81d13826c5b10da107695f287293765caddf45;hpb=7b999e54e654437cdd7d341bded0be02c10fc917;p=jalview.git diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java index 2f81d13..500047b 100755 --- a/src/jalview/schemes/ColourSchemeProperty.java +++ b/src/jalview/schemes/ColourSchemeProperty.java @@ -1,83 +1,110 @@ /* - * 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 + * 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. - * - * 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 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 + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ 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 ) + * 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; - /** Undefined Colourscheme Index */ - public static final int UNDEFINED = 13; - + /** + * 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! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -129,6 +156,11 @@ public class ColourSchemeProperty { ret = NUCLEOTIDE; } + else if (name.equalsIgnoreCase("T-Coffee Scores")) + { + ret = TCOFFEE; + } + else if (name.equalsIgnoreCase("User Defined")) { ret = USER_DEFINED; @@ -137,6 +169,22 @@ public class ColourSchemeProperty { 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; } @@ -145,7 +193,7 @@ public class ColourSchemeProperty * DOCUMENT ME! * * @param cs - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -198,6 +246,21 @@ public class ColourSchemeProperty { 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) @@ -216,7 +279,7 @@ public class ColourSchemeProperty * DOCUMENT ME! * * @param index - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -280,6 +343,29 @@ public class ColourSchemeProperty 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"; @@ -295,71 +381,78 @@ public class ColourSchemeProperty } /** - * 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! + * 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, + public static ColourSchemeI getColour(AnnotatedCollectionI alignment, String name) { int colindex = getColourIndexFromName(name); - if (colindex == UNDEFINED) // 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)); + 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! + * 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) + 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; @@ -412,6 +505,23 @@ public class ColourSchemeProperty 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++) @@ -487,4 +597,41 @@ public class ColourSchemeProperty 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; + } + }