X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FUserColourScheme.java;h=80efaca4e85a862fa9dd15b3c4c05104246de912;hb=ae21643b1d2aa912f1de8b7b0ce3e388860a5493;hp=ab9ad2fd75ce3dc0363f24cdb31143d52deb68f2;hpb=681588b5dfb7e3ff34ceaccdf47f2dae6bd590ce;p=jalview.git

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index ab9ad2f..80efaca 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -1,44 +1,68 @@
 /*
- * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.schemes;
 
-import java.util.*;
+import java.awt.Color;
+import java.util.Map;
+import java.util.StringTokenizer;
 
-import java.awt.*;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
 
-public class UserColourScheme
-    extends ResidueColourScheme
+public class UserColourScheme extends ResidueColourScheme
 {
   Color[] lowerCaseColours;
 
   protected String schemeName;
 
   public UserColourScheme()
-  {}
+  {
+    super(ResidueProperties.aaIndex);
+  }
 
   public UserColourScheme(Color[] newColors)
   {
+    super(ResidueProperties.aaIndex);
     colors = newColors;
   }
 
+  @Override
+  public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+  {
+    UserColourScheme usc = new UserColourScheme(colors);
+    if (lowerCaseColours != null)
+    {
+      usc.schemeName = new String(schemeName);
+      usc.lowerCaseColours = new Color[lowerCaseColours.length];
+      System.arraycopy(lowerCaseColours, 0, usc.lowerCaseColours, 0,
+              lowerCaseColours.length);
+    }
+    return usc;
+  }
+
   public UserColourScheme(String colour)
   {
+    super(ResidueProperties.aaIndex);
     Color col = getColourFromString(colour);
 
     if (col == null)
@@ -84,9 +108,9 @@ public class UserColourScheme
     {
       int value = Integer.parseInt(colour, 16);
       col = new Color(value);
+    } catch (NumberFormatException ex)
+    {
     }
-    catch (NumberFormatException ex)
-    {}
 
     if (col == null)
     {
@@ -97,15 +121,15 @@ 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;
@@ -140,6 +164,8 @@ public class UserColourScheme
 
   public void parseAppletParameter(String paramValue)
   {
+    // TODO: need a function to generate appletParameter colour string from a
+    // UCS
     StringTokenizer st = new StringTokenizer(paramValue, ";");
     StringTokenizer st2;
     String token = null, colour, residues;
@@ -194,21 +220,21 @@ 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, SequenceI seq)
   {
     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')
       {