From 681588b5dfb7e3ff34ceaccdf47f2dae6bd590ce Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 18 Jul 2008 12:30:57 +0000 Subject: [PATCH] User defined colourschemes are automatically generated from colour names or RGB colour triplets --- src/jalview/schemes/ColourSchemeProperty.java | 935 +++++++++++++------------ src/jalview/schemes/UserColourScheme.java | 479 ++++++------- 2 files changed, 723 insertions(+), 691 deletions(-) diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java index d3325ca..ef2feac 100755 --- a/src/jalview/schemes/ColourSchemeProperty.java +++ b/src/jalview/schemes/ColourSchemeProperty.java @@ -1,452 +1,483 @@ -/* - * 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 - * 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 -{ - /** 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) - { - 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; - } - - /** - * DOCUMENT ME! - * - * @param cs DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public static String getColourName(ColourSchemeI cs) - { - - 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); - } - - /** - * 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; - } -} +/* + * 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 + * 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.*; + +/** + * 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 ) + * + * @author $author$ + * @version $Revision$ + */ +public class ColourSchemeProperty +{ + /** 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) + { + 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; + } + + /** + * DOCUMENT ME! + * + * @param cs + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public static String getColourName(ColourSchemeI cs) + { + + 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) + { + if ((((UserColourScheme) cs).getName() != null) + && (((UserColourScheme) cs).getName().length() > 0)) + { + return ((UserColourScheme) cs).getName(); + } + // get default colourscheme name + index = USER_DEFINED; + } + + return getColourName(index); + } + + /** + * 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) + { + int colindex = getColourIndexFromName(name); + if (colindex > USER_DEFINED) + { + try + { + return new UserColourScheme(name); + } catch (Exception e) + { + // System.err.println("Ignoring unknown colourscheme 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; + } +} diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java index 81947b3..ab9ad2f 100755 --- a/src/jalview/schemes/UserColourScheme.java +++ b/src/jalview/schemes/UserColourScheme.java @@ -1,239 +1,240 @@ -/* - * 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 - * 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.util.*; - -import java.awt.*; - -public class UserColourScheme - extends ResidueColourScheme -{ - Color[] lowerCaseColours; - - protected String schemeName; - - public UserColourScheme() - {} - - public UserColourScheme(Color[] newColors) - { - colors = newColors; - } - - public UserColourScheme(String colour) - { - Color col = getColourFromString(colour); - - if (col == null) - { - System.out.println("Unknown colour!! " + colour); - col = createColourFromName(colour); - } - - colors = new Color[24]; - for (int i = 0; i < 24; i++) - { - colors[i] = col; - } - } - - public Color[] getColours() - { - return colors; - } - - public Color[] getLowerCaseColours() - { - return lowerCaseColours; - } - - public void setName(String name) - { - schemeName = name; - } - - public String getName() - { - return schemeName; - } - - public Color getColourFromString(String colour) - { - colour = colour.trim(); - - Color col = null; - try - { - int value = Integer.parseInt(colour, 16); - col = new Color(value); - } - catch (NumberFormatException ex) - {} - - if (col == null) - { - col = ColourSchemeProperty.getAWTColorFromName(colour); - } - - if (col == null) - { - try - { - java.util.StringTokenizer st = new java.util.StringTokenizer(colour, - ","); - int r = Integer.parseInt(st.nextToken()); - int g = Integer.parseInt(st.nextToken()); - int b = Integer.parseInt(st.nextToken()); - col = new Color(r, g, b); - } - catch (Exception ex) - {} - } - - return col; - - } - - public Color createColourFromName(String name) - { - int r, g, b; - - int lsize = name.length(); - int start = 0, end = lsize / 3; - - int rgbOffset = Math.abs(name.hashCode() % 10) * 15; - - r = Math.abs(name.substring(start, end).hashCode() + rgbOffset) % 210 + 20; - start = end; - end += lsize / 3; - if (end > lsize) - { - end = lsize; - } - - g = Math.abs(name.substring(start, end).hashCode() + rgbOffset) % 210 + 20; - - b = Math.abs(name.substring(end).hashCode() + rgbOffset) % 210 + 20; - - Color color = new Color(r, g, b); - - return color; - } - - public void parseAppletParameter(String paramValue) - { - StringTokenizer st = new StringTokenizer(paramValue, ";"); - StringTokenizer st2; - String token = null, colour, residues; - try - { - while (st.hasMoreElements()) - { - token = st.nextToken().trim(); - residues = token.substring(0, token.indexOf("=")); - colour = token.substring(token.indexOf("=") + 1); - - st2 = new StringTokenizer(residues, " ,"); - while (st2.hasMoreTokens()) - { - token = st2.nextToken(); - - if (ResidueProperties.aaIndex[token.charAt(0)] == -1) - { - continue; - } - - int colIndex = ResidueProperties.aaIndex[token.charAt(0)]; - - if (token.equalsIgnoreCase("lowerCase")) - { - if (lowerCaseColours == null) - { - lowerCaseColours = new Color[23]; - } - for (int i = 0; i < 23; i++) - { - if (lowerCaseColours[i] == null) - { - lowerCaseColours[i] = getColourFromString(colour); - } - } - - continue; - } - - if (token.equals(token.toLowerCase())) - { - if (lowerCaseColours == null) - { - lowerCaseColours = new Color[23]; - } - lowerCaseColours[colIndex] = getColourFromString(colour); - } - else - { - colors[colIndex] = getColourFromString(colour); - } - } - } - } - catch (Exception ex) - { - System.out.println("Error parsing userDefinedColours:\n" - + token + "\n" + ex); - } - - } - - public Color findColour(char c, int j) - { - Color currentColour; - int index = ResidueProperties.aaIndex[c]; - - if ( (threshold == 0) || aboveThreshold(c, j)) - { - if (lowerCaseColours != null && 'a' <= c && c <= 'z') - { - currentColour = lowerCaseColours[index]; - } - else - { - currentColour = colors[index]; - } - } - else - { - currentColour = Color.white; - } - - if (conservationColouring) - { - currentColour = applyConservation(currentColour, j); - } - - return currentColour; - } - - public void setLowerCaseColours(Color[] lcolours) - { - lowerCaseColours = lcolours; - } - -} +/* + * 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 + * 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.util.*; + +import java.awt.*; + +public class UserColourScheme + extends ResidueColourScheme +{ + Color[] lowerCaseColours; + + protected String schemeName; + + public UserColourScheme() + {} + + public UserColourScheme(Color[] newColors) + { + colors = newColors; + } + + public UserColourScheme(String colour) + { + Color col = getColourFromString(colour); + + if (col == null) + { + System.out.println("Unknown colour!! " + colour); + col = createColourFromName(colour); + } + + colors = new Color[24]; + for (int i = 0; i < 24; i++) + { + colors[i] = col; + } + schemeName = colour; + } + + public Color[] getColours() + { + return colors; + } + + public Color[] getLowerCaseColours() + { + return lowerCaseColours; + } + + public void setName(String name) + { + schemeName = name; + } + + public String getName() + { + return schemeName; + } + + public Color getColourFromString(String colour) + { + colour = colour.trim(); + + Color col = null; + try + { + int value = Integer.parseInt(colour, 16); + col = new Color(value); + } + catch (NumberFormatException ex) + {} + + if (col == null) + { + col = ColourSchemeProperty.getAWTColorFromName(colour); + } + + if (col == null) + { + try + { + java.util.StringTokenizer st = new java.util.StringTokenizer(colour, + ","); + int r = Integer.parseInt(st.nextToken()); + int g = Integer.parseInt(st.nextToken()); + int b = Integer.parseInt(st.nextToken()); + col = new Color(r, g, b); + } + catch (Exception ex) + {} + } + + return col; + + } + + public Color createColourFromName(String name) + { + int r, g, b; + + int lsize = name.length(); + int start = 0, end = lsize / 3; + + int rgbOffset = Math.abs(name.hashCode() % 10) * 15; + + r = Math.abs(name.substring(start, end).hashCode() + rgbOffset) % 210 + 20; + start = end; + end += lsize / 3; + if (end > lsize) + { + end = lsize; + } + + g = Math.abs(name.substring(start, end).hashCode() + rgbOffset) % 210 + 20; + + b = Math.abs(name.substring(end).hashCode() + rgbOffset) % 210 + 20; + + Color color = new Color(r, g, b); + + return color; + } + + public void parseAppletParameter(String paramValue) + { + StringTokenizer st = new StringTokenizer(paramValue, ";"); + StringTokenizer st2; + String token = null, colour, residues; + try + { + while (st.hasMoreElements()) + { + token = st.nextToken().trim(); + residues = token.substring(0, token.indexOf("=")); + colour = token.substring(token.indexOf("=") + 1); + + st2 = new StringTokenizer(residues, " ,"); + while (st2.hasMoreTokens()) + { + token = st2.nextToken(); + + if (ResidueProperties.aaIndex[token.charAt(0)] == -1) + { + continue; + } + + int colIndex = ResidueProperties.aaIndex[token.charAt(0)]; + + if (token.equalsIgnoreCase("lowerCase")) + { + if (lowerCaseColours == null) + { + lowerCaseColours = new Color[23]; + } + for (int i = 0; i < 23; i++) + { + if (lowerCaseColours[i] == null) + { + lowerCaseColours[i] = getColourFromString(colour); + } + } + + continue; + } + + if (token.equals(token.toLowerCase())) + { + if (lowerCaseColours == null) + { + lowerCaseColours = new Color[23]; + } + lowerCaseColours[colIndex] = getColourFromString(colour); + } + else + { + colors[colIndex] = getColourFromString(colour); + } + } + } + } + catch (Exception ex) + { + System.out.println("Error parsing userDefinedColours:\n" + + token + "\n" + ex); + } + + } + + public Color findColour(char c, int j) + { + Color currentColour; + int index = ResidueProperties.aaIndex[c]; + + if ( (threshold == 0) || aboveThreshold(c, j)) + { + if (lowerCaseColours != null && 'a' <= c && c <= 'z') + { + currentColour = lowerCaseColours[index]; + } + else + { + currentColour = colors[index]; + } + } + else + { + currentColour = Color.white; + } + + if (conservationColouring) + { + currentColour = applyConservation(currentColour, j); + } + + return currentColour; + } + + public void setLowerCaseColours(Color[] lcolours) + { + lowerCaseColours = lcolours; + } + +} -- 1.7.10.2