X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FUserColourScheme.java;h=d55ffbfb06d0c55e7bbea3e92c1eac1fca0b955f;hb=dd2acb4e1060219d28f3acbe34772b947a6a4547;hp=cdc618e7a983e077fab09e096ede8320d447825e;hpb=a79f9e113c51c032070c670e45ce3eb464691166;p=jalview.git
diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index cdc618e..d55ffbf 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -1,57 +1,142 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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
+ * 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) { - int r, g, b; + setAll(Color.white); - 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; @@ -153,87 +192,169 @@ 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(Locale.ROOT))) { 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 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 Color findColour(char c, int j, SequenceI seq) + 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() { - Color currentColour; - int index = ResidueProperties.aaIndex[c]; + /* + * step 1: build a map from colours to the symbol(s) that have the colour + */ + Map