X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=0123384d0152edc8314bfc1c1a25c68539769293;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=8317bd7c09daf9666060e07be5670b1ec4699c9d;hpb=66b1bf1a6480b320ddaa00d4f5e70b2051041c11;p=jalview.git diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java index 8317bd7..0123384 100755 --- a/src/jalview/schemes/ColourSchemeProperty.java +++ b/src/jalview/schemes/ColourSchemeProperty.java @@ -1,129 +1,125 @@ -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, getColourIndexFromName(name)); - } - - public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, int index) - { - ColourSchemeI cs = null; - switch(index) - { - 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: 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; + +/** + * 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 +{ + + private ColourSchemeProperty() + { + // requires static call to getColourScheme(...). + } + + /** + * 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; + } + + /** + * 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(); + } + +}