merge from 2_4_Release branch

[jalview.git] / src / jalview / schemes / UserColourScheme.java

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index ab9ad2f..e42fd29 100755 (executable)
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
@@ -22,15 +22,15 @@ import java.util.*;
 
 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 +84,9 @@ public class UserColourScheme
     {
       int value = Integer.parseInt(colour, 16);
       col = new Color(value);
+    } catch (NumberFormatException ex)
+    {
     }
-    catch (NumberFormatException ex)
-    {}
 
     if (col == null)
     {
@@ -97,15 +97,15 @@ 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;
@@ -194,11 +194,10 @@ 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);
     }
 
   }
@@ -208,7 +207,7 @@ public class UserColourScheme
     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')
       {