X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fschemes%2FUserColourScheme.java;h=d77f2f53d4d663e1e0ead2b883960d688f4dea72;hb=72943d968f678ca4e34f1b701823d6dab51ff3a2;hp=38a12910e1a842a65fc455ef1eb957e6e919f969;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git
diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 38a1291..d77f2f5 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -1,32 +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(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
+ * 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