X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FUserColourScheme.java;h=d77f2f53d4d663e1e0ead2b883960d688f4dea72;hb=136df5f299843e2b21dcc3d37a1d7523a322e0e0;hp=ab9ad2fd75ce3dc0363f24cdb31143d52deb68f2;hpb=681588b5dfb7e3ff34ceaccdf47f2dae6bd590ce;p=jalview.git
diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index ab9ad2f..d77f2f5 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -1,58 +1,140 @@
/*
- * 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
+ * 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.
- *
- * 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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; @@ -154,87 +190,169 @@ public class UserColourScheme 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); } - catch (Exception 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) { - System.out.println("Error parsing userDefinedColours:\n" - + token + "\n" + ex); + 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; } - public Color findColour(char c, int j) + /** + * 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