X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=278cf6afcafad8b8de0d3f8c2cdc364ca805bfa1;hb=51bbc79eee43d019f9fcb14b7aa6e0a0c2c99f76;hp=4343b54ecbbda59f6eaa1d8b1d96866d8db955e7;hpb=a0dfca2ab49882cb8544d16cd105faaaf9f2ef10;p=jalview.git diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java index 4343b54..278cf6a 100755 --- a/src/jalview/schemes/ColourSchemeProperty.java +++ b/src/jalview/schemes/ColourSchemeProperty.java @@ -1,133 +1,424 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2006 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; +import java.awt.*; +/** + * DOCUMENT ME! + * + * @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 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) + /** DOCUMENT ME!! */ + public static final int CLUSTAL = 0; + + /** DOCUMENT ME!! */ + public static final int BLOSUM = 1; + + /** DOCUMENT ME!! */ + public static final int PID = 2; + + /** DOCUMENT ME!! */ + public static final int ZAPPO = 3; + + /** DOCUMENT ME!! */ + public static final int TAYLOR = 4; + + /** DOCUMENT ME!! */ + public static final int HYDROPHOBIC = 5; + + /** DOCUMENT ME!! */ + public static final int HELIX = 6; + + /** DOCUMENT ME!! */ + public static final int STRAND = 7; + + /** DOCUMENT ME!! */ + public static final int TURN = 8; + + /** DOCUMENT ME!! */ + public static final int BURIED = 9; + + /** DOCUMENT ME!! */ + public static final int NUCLEOTIDE = 10; + + /** DOCUMENT ME!! */ + public static final int USER_DEFINED = 11; + + + /** DOCUMENT ME!! */ + public static final int NONE = 12; + + /** + * DOCUMENT ME! + * + * @param name DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public static int getColourIndexFromName(String 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; + int ret = 12; + + 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("Taylor")) + { + ret = TAYLOR; + } + 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; } - 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) + + /** + * DOCUMENT ME! + * + * @param cs DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public static String getColourName(ColourSchemeI cs) { - 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; + + int index = 12; + + 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 TaylorColourScheme) + { + index = TAYLOR; + } + 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); } - return cs; - } + /** + * DOCUMENT ME! + * + * @param index DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + 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 TAYLOR: + ret = "Taylor"; + 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; + } + + /** + * 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! + * + * @param seqs DOCUMENT ME! + * @param width DOCUMENT ME! + * @param name DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public static ColourSchemeI getColour(java.util.Vector seqs, int width, + String name) + { + return getColour(seqs, width, getColourIndexFromName(name)); + } + + /** + * DOCUMENT ME! + * + * @param seqs DOCUMENT ME! + * @param width DOCUMENT ME! + * @param index DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + 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 TAYLOR: + cs = new TaylorColourScheme(); + 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: + Color[] col = new Color[24]; + for (int i = 0; i < 24; i++) + col[i] = Color.white; + cs = new UserColourScheme(col); + break; + + default: + break; + } + + return cs; + } + + public static Color getAWTColorFromName(String name) + { + Color col = null; + name = name.toLowerCase(); + if(name.equals("black")) + col = Color.black; + else if(name.equals("blue")) + col = Color.blue; + else if(name.equals("cyan")) + col = Color.cyan; + else if(name.equals("darkGray")) + col = Color.darkGray; + else if(name.equals("gray")) + col = Color.gray; + else if(name.equals("green")) + col = Color.green; + else if(name.equals("lightGray")) + col = Color.lightGray; + else if(name.equals("magenta")) + col = Color.magenta; + else if(name.equals("orange")) + col = Color.orange; + else if(name.equals("pink")) + col = Color.pink; + else if(name.equals("red")) + col = Color.red; + else if(name.equals("white")) + col = Color.white; + else if(name.equals("yellow")) + col = Color.yellow; + + return col; + } }