X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FUserColourScheme.java;h=0c1e688f7a2f747ae387adef0fe2e1af8bcf687c;hb=b65e8427808280faf920f306f7f0e5a71a9ff6bf;hp=ab9ad2fd75ce3dc0363f24cdb31143d52deb68f2;hpb=681588b5dfb7e3ff34ceaccdf47f2dae6bd590ce;p=jalview.git

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index ab9ad2f..0c1e688 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -1,36 +1,34 @@
 /*
- * 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
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * 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 <http://www.gnu.org/licenses/>.
  */
 package jalview.schemes;
 
-import java.util.*;
+import java.awt.Color;
+import java.util.StringTokenizer;
 
-import java.awt.*;
-
-public class UserColourScheme
-    extends ResidueColourScheme
+public class UserColourScheme extends ResidueColourScheme
 {
   Color[] lowerCaseColours;
 
   protected String schemeName;
 
   public UserColourScheme()
-  {}
+  {
+  }
 
   public UserColourScheme(Color[] newColors)
   {
@@ -84,9 +82,9 @@ public class UserColourScheme
     {
       int value = Integer.parseInt(colour, 16);
       col = new Color(value);
+    } catch (NumberFormatException ex)
+    {
     }
-    catch (NumberFormatException ex)
-    {}
 
     if (col == null)
     {
@@ -97,15 +95,15 @@ public class UserColourScheme
     {
       try
       {
-        java.util.StringTokenizer st = new java.util.StringTokenizer(colour,
-            ",");
+        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)
+      {
       }
-      catch (Exception ex)
-      {}
     }
 
     return col;
@@ -194,21 +192,21 @@ public class UserColourScheme
           }
         }
       }
-    }
-    catch (Exception ex)
+    } 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)
+  @Override
+  public Color findColour(char c, int j, int sequenceIndex)
   {
     Color currentColour;
     int index = ResidueProperties.aaIndex[c];
 
-    if ( (threshold == 0) || aboveThreshold(c, j))
+    if ((threshold == 0) || aboveThreshold(c, j))
     {
       if (lowerCaseColours != null && 'a' <= c && c <= 'z')
       {