X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemes.java;h=d31fbba4c752c19aaffd3be8c6def41e13b3c1ac;hb=f3fa435d421eb9f071a526f802801c4a21ee2dc4;hp=21faa2a43e8165817df5be5d1468c530931eadc3;hpb=94379c810f9115b8564ee7bac46ed119218d5fd2;p=jalview.git

diff --git a/src/jalview/schemes/ColourSchemes.java b/src/jalview/schemes/ColourSchemes.java
index 21faa2a..d31fbba 100644
--- a/src/jalview/schemes/ColourSchemes.java
+++ b/src/jalview/schemes/ColourSchemes.java
@@ -1,7 +1,29 @@
+/*
+ * 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 jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
 
 import java.util.LinkedHashMap;
 import java.util.Map;
@@ -14,7 +36,7 @@ public class ColourSchemes
   private static ColourSchemes instance = new ColourSchemes();
 
   /*
-   * a map from scheme name to an instance of it
+   * a map from scheme name (lower-cased) to an instance of it
    */
   private Map<String, ColourSchemeI> schemes;
 
@@ -44,17 +66,22 @@ 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();
       }
     }
   }
@@ -93,9 +120,12 @@ public class ColourSchemes
    */
   public void removeColourScheme(String name)
   {
-    schemes.remove(name);
+    if (name != null)
+    {
+      schemes.remove(name.toLowerCase());
+    }
   }
-  
+
   /**
    * Returns an instance of the colour scheme with which the given view may be
    * coloured
@@ -103,32 +133,40 @@ public class ColourSchemes
    * @param name
    *          name of the colour scheme
    * @param viewport
+   * @param forData
+   *          the data to be coloured
+   * @param optional
+   *          map from hidden representative sequences to the sequences they
+   *          represent
    * @return
    */
-  public ColourSchemeI getColourScheme(String name, AlignViewportI viewport)
+  public ColourSchemeI getColourScheme(String name,
+          AlignViewportI viewport, AnnotatedCollectionI forData,
+          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
     if (name == null)
     {
       return null;
     }
     ColourSchemeI cs = schemes.get(name.toLowerCase());
-    return cs == null ? null : cs.getInstance(viewport.getAlignment(),
-            viewport.getHiddenRepSequences());
+    return cs == null ? null
+            : cs.getInstance(viewport, forData);
   }
 
   /**
-   * Returns an instance of the colour scheme with which the given data may be
+   * Returns an instance of the colour scheme with which the given view may be
    * coloured
    * 
    * @param name
+   *          name of the colour scheme
    * @param forData
+   *          the data to be coloured
    * @return
    */
   public ColourSchemeI getColourScheme(String name,
           AnnotatedCollectionI forData)
   {
-    ColourSchemeI cs = schemes.get(name.toLowerCase());
-    return cs == null ? null : cs.getInstance(forData, null);
+    return getColourScheme(name, null, forData, null);
   }
 
   /**
@@ -141,4 +179,20 @@ public class ColourSchemes
   {
     return schemes.values();
   }
+
+  /**
+   * Answers true if there is a scheme with the given name, else false. The test
+   * is not case-sensitive.
+   * 
+   * @param name
+   * @return
+   */
+  public boolean nameExists(String name)
+  {
+    if (name == null)
+    {
+      return false;
+    }
+    return schemes.containsKey(name.toLowerCase());
+  }
 }