X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FUserColourScheme.java;h=d77f2f53d4d663e1e0ead2b883960d688f4dea72;hb=4d959452a9c486b6d94291d8e819036ec19b09ef;hp=9b0133211f67f2dc8d8760e8dbcc8164ea3939a7;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java index 9b01332..d77f2f5 100755 --- a/src/jalview/schemes/UserColourScheme.java +++ b/src/jalview/schemes/UserColourScheme.java @@ -1,57 +1,140 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * 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. - * + * 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 . + * 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 java.util.*; +import jalview.api.AlignViewportI; +import jalview.datamodel.AnnotatedCollectionI; +import jalview.util.ColorUtils; +import jalview.util.StringUtils; -import java.awt.*; +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) { - Color col = getColourFromString(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("Unknown colour!! " + colour); - col = createColourFromName(colour); + System.out.println("Making colour from name: " + colour); + col = ColorUtils.createColourFromName(colour); } - colors = new Color[24]; - for (int i = 0; i < 24; i++) + 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; } - schemeName = colour; } public Color[] getColours() @@ -74,71 +157,25 @@ public class UserColourScheme extends ResidueColourScheme return schemeName; } - public Color getColourFromString(String colour) + /** + * 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) { - 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; + setAll(Color.white); - 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; @@ -153,86 +190,169 @@ public class UserColourScheme extends ResidueColourScheme st2 = new StringTokenizer(residues, " ,"); while (st2.hasMoreTokens()) { - token = st2.nextToken(); + String residue = st2.nextToken(); - if (ResidueProperties.aaIndex[token.charAt(0)] == -1) + int colIndex = ResidueProperties.aaIndex[residue.charAt(0)]; + if (colIndex == -1) { continue; } - int colIndex = ResidueProperties.aaIndex[token.charAt(0)]; - - if (token.equalsIgnoreCase("lowerCase")) + if (residue.equalsIgnoreCase("lowerCase")) { if (lowerCaseColours == null) { - lowerCaseColours = new Color[23]; + lowerCaseColours = new Color[colors.length]; } - for (int i = 0; i < 23; i++) + for (int i = 0; i < lowerCaseColours.length; i++) { if (lowerCaseColours[i] == null) { - lowerCaseColours[i] = getColourFromString(colour); + lowerCaseColours[i] = ColorUtils.parseColourString(colour); } } continue; } - if (token.equals(token.toLowerCase())) + if (residue.equals(residue.toLowerCase())) { if (lowerCaseColours == null) { - lowerCaseColours = new Color[23]; + lowerCaseColours = new Color[colors.length]; } - lowerCaseColours[colIndex] = getColourFromString(colour); + lowerCaseColours[colIndex] = ColorUtils + .parseColourString(colour); } else { - colors[colIndex] = getColourFromString(colour); + colors[colIndex] = ColorUtils.parseColourString(colour); } } } } catch (Exception ex) { - System.out.println("Error parsing userDefinedColours:\n" + token - + "\n" + ex); + System.out.println( + "Error parsing userDefinedColours:\n" + token + "\n" + ex); } } - public Color findColour(char c, int j) + public void setLowerCaseColours(Color[] lcolours) { - Color currentColour; - int index = ResidueProperties.aaIndex[c]; + lowerCaseColours = lcolours; + } - if ((threshold == 0) || aboveThreshold(c, j)) + /** + * 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) { - if (lowerCaseColours != null && 'a' <= c && c <= 'z') - { - currentColour = lowerCaseColours[index]; - } - else + Color colour = lowerCaseColours[symbolIndex[c]]; + if (colour != null) { - currentColour = colors[index]; + return colour; } } - else + 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) { - currentColour = Color.white; + return schemeName; } + return ResidueColourScheme.USER_DEFINED; + } - if (conservationColouring) + /** + * 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++) { - currentColour = applyConservation(currentColour, j); + 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); + } + } } - return currentColour; + /* + * 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, ";"); } - public void setLowerCaseColours(Color[] lcolours) + @Override + public boolean hasGapColour() { - lowerCaseColours = lcolours; + return (findColour(' ') != null); } - }