X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=98e90bdf769f07363b4b8bb598d97a5edf6d3db2;hb=b9b1f47cc74bbec8c28b75776e1d00c258215dfb;hp=0d5ecc7b1478aff8a9a6bd1f56edcef8efa938d6;hpb=6bd69f196a5bdb8bdbc329166485d5da60b27389;p=jalview.git diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java index 0d5ecc7..98e90bd 100755 --- a/src/jalview/schemes/ColourSchemeProperty.java +++ b/src/jalview/schemes/ColourSchemeProperty.java @@ -1,243 +1,156 @@ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 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 -*/ -package jalview.schemes; - -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 int getColourIndexFromName(String name) { - int ret = 11; - - if (name.equalsIgnoreCase("Clustal")) { - ret = CLUSTAL; - } else if (name.equalsIgnoreCase("Blosum62")) { - ret = BLOSUM; - } else if (name.equalsIgnoreCase("% Identity")) { - ret = PID; - } else if (name.equalsIgnoreCase("Zappo")) { - ret = ZAPPO; - } else if (name.equalsIgnoreCase("Hydrophobic")) { - ret = HYDROPHOBIC; - } else if (name.equalsIgnoreCase("Helix Propensity")) { - ret = HELIX; - } else if (name.equalsIgnoreCase("Strand Propensity")) { - ret = STRAND; - } else if (name.equalsIgnoreCase("Turn Propensity")) { - ret = TURN; - } else if (name.equalsIgnoreCase("Buried Index")) { - ret = BURIED; - } else if (name.equalsIgnoreCase("Nucleotide")) { - ret = NUCLEOTIDE; - } else if (name.equalsIgnoreCase("User Defined")) { - ret = USER_DEFINED; - } - - return ret; - } - - public static String getColourName(ColourSchemeI cs) { - if (cs instanceof ConservationColourScheme) { - cs = ((ConservationColourScheme) cs).cs; - } - - int index = 11; - - if (cs instanceof ClustalxColourScheme) { - index = CLUSTAL; - } else if (cs instanceof Blosum62ColourScheme) { - index = BLOSUM; - } else if (cs instanceof PIDColourScheme) { - index = PID; - } else if (cs instanceof ZappoColourScheme) { - index = ZAPPO; - } else if (cs instanceof HydrophobicColourScheme) { - index = HYDROPHOBIC; - } else if (cs instanceof HelixColourScheme) { - index = HELIX; - } else if (cs instanceof StrandColourScheme) { - index = STRAND; - } else if (cs instanceof TurnColourScheme) { - index = TURN; - } else if (cs instanceof BuriedColourScheme) { - index = BURIED; - } else if (cs instanceof NucleotideColourScheme) { - index = NUCLEOTIDE; - } else if (cs instanceof UserColourScheme) { - index = USER_DEFINED; - } - - return getColourName(index); - } - - public static String getColourName(int index) { - String ret = null; - - switch (index) { - 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 ret; - } - - public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, String name) - { - return getColour(al.getSequences(), al.getWidth(), name); - } - - public static ColourSchemeI getColour(java.util.Vector seqs, int width, - String name) { - return getColour(seqs, width, getColourIndexFromName(name)); - } - - public static ColourSchemeI getColour(java.util.Vector seqs, int width, - int index) { - ColourSchemeI cs = null; - - switch (index) { - case CLUSTAL: - cs = new ClustalxColourScheme(seqs, width); - - 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: - cs = new UserColourScheme(null); - - break; - - default: - break; - } - - return cs; - } -} +/* + * 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 +{ + + /** + * 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) + { + if (ResidueColourScheme.NONE.equalsIgnoreCase(name)) + { + return null; + + } + + /* + * 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) + { + return scheme; + } + + /* + * 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 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] = ColorUtils.generateRandomColor(Color.white); + } + } + + /** + * 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(); + } + +}