X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FUserColourScheme.java;h=d77f2f53d4d663e1e0ead2b883960d688f4dea72;hb=4d959452a9c486b6d94291d8e819036ec19b09ef;hp=7bd61c1efd665a505ca4c213ad3453780386e206;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java index 7bd61c1..d77f2f5 100755 --- a/src/jalview/schemes/UserColourScheme.java +++ b/src/jalview/schemes/UserColourScheme.java @@ -1,57 +1,358 @@ -/* - * 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; - -import java.awt.*; - -public class UserColourScheme - extends ResidueColourScheme -{ - public UserColourScheme(String colour) - { - 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) - { - System.out.println("Unknown colour!! "+colour); - } - - colors = new Color[24]; - for(int i=0; i<24; i++) - colors[i] = col; - } - - public UserColourScheme(Color[] newColors) - { - colors = newColors; - } - - public Color[] getColours() - { - return colors; - } -} +/* + * 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 jalview.util.StringUtils; + +import java.awt.Color; +import java.util.ArrayList; +import java.util.Collections; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.Map.Entry; +import java.util.StringTokenizer; + +public class UserColourScheme extends ResidueColourScheme +{ + /* + * lookup (by symbol index) of lower case colours (if configured) + */ + Color[] lowerCaseColours; + + protected String schemeName; + + public UserColourScheme() + { + super(ResidueProperties.aaIndex); + } + + public UserColourScheme(Color[] newColors) + { + super(ResidueProperties.aaIndex); + colors = newColors; + } + + @Override + public ColourSchemeI getInstance(AlignViewportI view, + AnnotatedCollectionI sg) + { + return new UserColourScheme(this); + } + + /** + * Copy constructor + * + * @return + */ + protected UserColourScheme(UserColourScheme from) + { + this(from.colors); + schemeName = from.schemeName; + if (from.lowerCaseColours != null) + { + lowerCaseColours = new Color[from.lowerCaseColours.length]; + System.arraycopy(from.lowerCaseColours, 0, lowerCaseColours, 0, + from.lowerCaseColours.length); + } + } + + /** + * Constructor for an animino acid colour scheme. The colour specification may + * be one of + * + * + * @param colour + */ + public UserColourScheme(String colour) + { + super(ResidueProperties.aaIndex); + + if (colour.contains("=")) + { + /* + * a list of colours per residue(s) + */ + parseAppletParameter(colour); + return; + } + + Color col = ColorUtils.parseColourString(colour); + + if (col == null) + { + System.out.println("Making colour from name: " + colour); + col = ColorUtils.createColourFromName(colour); + } + + setAll(col); + schemeName = colour; + } + + /** + * Sets all symbols to the specified colour + * + * @param col + */ + protected void setAll(Color col) + { + if (symbolIndex == null) + { + return; + } + int max = 0; + for (int index : symbolIndex) + { + max = Math.max(max, index); + } + colors = new Color[max + 1]; + for (int i = 0; i <= max; 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; + } + + /** + * Parse and save residue colours specified as (for example) + * + * 
+   *     D,E=red; K,R,H=0022FF; c=100,50,75
+   *
+ * + * This should be a semi-colon separated list of colours, which may be defined + * by colour name, hex value or comma-separated RGB triple. Each colour is + * defined for a comma-separated list of amino acid single letter codes. (Note + * that this also allows a colour scheme to be defined for ACGT, but not for + * U.) + * + * @param paramValue + */ + void parseAppletParameter(String paramValue) + { + setAll(Color.white); + + 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()) + { + String residue = st2.nextToken(); + + int colIndex = ResidueProperties.aaIndex[residue.charAt(0)]; + if (colIndex == -1) + { + continue; + } + + if (residue.equalsIgnoreCase("lowerCase")) + { + if (lowerCaseColours == null) + { + lowerCaseColours = new Color[colors.length]; + } + for (int i = 0; i < lowerCaseColours.length; i++) + { + if (lowerCaseColours[i] == null) + { + lowerCaseColours[i] = ColorUtils.parseColourString(colour); + } + } + + continue; + } + + if (residue.equals(residue.toLowerCase())) + { + if (lowerCaseColours == null) + { + lowerCaseColours = new Color[colors.length]; + } + lowerCaseColours[colIndex] = ColorUtils + .parseColourString(colour); + } + else + { + colors[colIndex] = ColorUtils.parseColourString(colour); + } + } + } + } catch (Exception ex) + { + System.out.println( + "Error parsing userDefinedColours:\n" + token + "\n" + ex); + } + + } + + public void setLowerCaseColours(Color[] lcolours) + { + lowerCaseColours = lcolours; + } + + /** + * Returns the colour for the given residue character. If the residue is + * lower-case, and there is a specific colour defined for lower case, that + * colour is returned, else the colour for the upper case residue. + */ + @Override + public Color findColour(char c) + { + if ('a' <= c && c <= 'z' && lowerCaseColours != null) + { + Color colour = lowerCaseColours[symbolIndex[c]]; + if (colour != null) + { + return colour; + } + } + return super.findColour(c); + } + + /** + * Answers the customised name of the colour scheme, if it has one, else "User + * Defined" + */ + @Override + public String getSchemeName() + { + if (schemeName != null && schemeName.length() > 0) + { + return schemeName; + } + return ResidueColourScheme.USER_DEFINED; + } + + /** + * Generate an applet colour parameter like A,C,D=12ffe9;Q,W=2393fd;w=9178dd + * + * @return + */ + public String toAppletParameter() + { + /* + * step 1: build a map from colours to the symbol(s) that have the colour + */ + Map> colours = new HashMap<>(); + + for (char symbol = 'A'; symbol <= 'Z'; symbol++) + { + String residue = String.valueOf(symbol); + int index = symbolIndex[symbol]; + Color c = colors[index]; + if (c != null && !c.equals(Color.white)) + { + if (colours.get(c) == null) + { + colours.put(c, new ArrayList()); + } + colours.get(c).add(residue); + } + if (lowerCaseColours != null) + { + c = lowerCaseColours[index]; + if (c != null && !c.equals(Color.white)) + { + residue = residue.toLowerCase(); + if (colours.get(c) == null) + { + colours.put(c, new ArrayList()); + } + colours.get(c).add(residue); + } + } + } + + /* + * step 2: make a list of { A,G,R=12f9d6 } residues/colour specs + */ + List residueColours = new ArrayList<>(); + for (Entry> cols : colours.entrySet()) + { + boolean first = true; + StringBuilder sb = new StringBuilder(); + for (String residue : cols.getValue()) + { + if (!first) + { + sb.append(","); + } + sb.append(residue); + first = false; + } + sb.append("="); + /* + * get color as hex value, dropping the alpha (ff) part + */ + String hexString = Integer.toHexString(cols.getKey().getRGB()) + .substring(2); + sb.append(hexString); + residueColours.add(sb.toString()); + } + + /* + * sort and output + */ + Collections.sort(residueColours); + return StringUtils.listToDelimitedString(residueColours, ";"); + } + + @Override + public boolean hasGapColour() + { + return (findColour(' ') != null); + } +}