X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemes.java;h=14daed6953f7d95f9258462f7d7a8d066b1cdd2a;hb=f721bbb9c300f6a1c845659b3947ebeca2795523;hp=b28139fd430454fe2bbf957e62b5f32def957fa1;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/schemes/ColourSchemes.java b/src/jalview/schemes/ColourSchemes.java
index b28139f..14daed6 100644
--- a/src/jalview/schemes/ColourSchemes.java
+++ b/src/jalview/schemes/ColourSchemes.java
@@ -1,5 +1,28 @@
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.schemes;
 
+import java.util.Locale;
+
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
@@ -45,17 +68,22 @@ public class ColourSchemes
      * store in an order-preserving map, so items can be added to menus 
      * in the order in which they are 'discovered'
      */
-    schemes = new LinkedHashMap<String, ColourSchemeI>();
+    schemes = new LinkedHashMap<>();
 
     for (JalviewColourScheme cs : JalviewColourScheme.values())
     {
       try
       {
-        registerColourScheme(cs.getSchemeClass().newInstance());
+        registerColourScheme(
+                cs.getSchemeClass().getDeclaredConstructor().newInstance());
       } catch (InstantiationException | IllegalAccessException e)
       {
         System.err.println("Error instantiating colour scheme for "
                 + cs.toString() + " " + e.getMessage());
+        e.printStackTrace();
+      } catch (ReflectiveOperationException roe)
+      {
+        roe.printStackTrace();
       }
     }
   }
@@ -78,7 +106,7 @@ public class ColourSchemes
      * name is lower-case for non-case-sensitive lookup
      * (name in the colour keeps its true case)
      */
-    String lower = name.toLowerCase();
+    String lower = name.toLowerCase(Locale.ROOT);
     if (schemes.containsKey(lower))
     {
       System.err
@@ -96,7 +124,7 @@ public class ColourSchemes
   {
     if (name != null)
     {
-      schemes.remove(name.toLowerCase());
+      schemes.remove(name.toLowerCase(Locale.ROOT));
     }
   }
 
@@ -106,6 +134,7 @@ public class ColourSchemes
    * 
    * @param name
    *          name of the colour scheme
+   * @param viewport
    * @param forData
    *          the data to be coloured
    * @param optional
@@ -113,7 +142,7 @@ public class ColourSchemes
    *          represent
    * @return
    */
-  public ColourSchemeI getColourScheme(String name,
+  public ColourSchemeI getColourScheme(String name, AlignViewportI viewport,
           AnnotatedCollectionI forData,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
@@ -121,8 +150,8 @@ public class ColourSchemes
     {
       return null;
     }
-    ColourSchemeI cs = schemes.get(name.toLowerCase());
-    return cs == null ? null : cs.getInstance(forData, hiddenRepSequences);
+    ColourSchemeI cs = schemes.get(name.toLowerCase(Locale.ROOT));
+    return cs == null ? null : cs.getInstance(viewport, forData);
   }
 
   /**
@@ -138,7 +167,7 @@ public class ColourSchemes
   public ColourSchemeI getColourScheme(String name,
           AnnotatedCollectionI forData)
   {
-    return getColourScheme(name, forData, null);
+    return getColourScheme(name, null, forData, null);
   }
 
   /**
@@ -165,6 +194,6 @@ public class ColourSchemes
     {
       return false;
     }
-    return schemes.containsKey(name.toLowerCase());
+    return schemes.containsKey(name.toLowerCase(Locale.ROOT));
   }
 }