X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemes.java;h=9e64e3393986a9b227ee7f2c204361c03427ba42;hb=df8e2545932852b0f257a3d67b33996afdfd259b;hp=269811b662dffe63be28098a3a5cc54f682059ad;hpb=1ddaca03529cd2b02502a1dae10c18582164972d;p=jalview.git

diff --git a/src/jalview/schemes/ColourSchemes.java b/src/jalview/schemes/ColourSchemes.java
index 269811b..9e64e33 100644
--- a/src/jalview/schemes/ColourSchemes.java
+++ b/src/jalview/schemes/ColourSchemes.java
@@ -1,23 +1,41 @@
+/*
+ * 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.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
+import jalview.util.ColorUtils;
 
+import java.awt.Color;
 import java.util.LinkedHashMap;
 import java.util.Map;
 
-public class ColourSchemes
+public class ColourSchemes implements ApplicationSingletonI
 {
-  /*
-   * singleton instance of this class
-   */
-  private static ColourSchemes instance = new ColourSchemes();
-
-  /*
-   * a map from scheme name (lower-cased) to an instance of it
-   */
-  private Map<String, ColourSchemeI> schemes;
 
   /**
    * Returns the singleton instance of this class
@@ -26,7 +44,7 @@ public class ColourSchemes
    */
   public static ColourSchemes getInstance()
   {
-    return instance;
+    return ApplicationSingletonProvider.getInstance(ColourSchemes.class);
   }
 
   private ColourSchemes()
@@ -35,6 +53,51 @@ public class ColourSchemes
   }
 
   /**
+   * ColourSchemeProperty "static"
+   */
+  public Color[] rnaHelices = null;
+
+  /**
+   * delete the existing cached RNA helices colours
+   */
+  public static void resetRnaHelicesShading()
+  {
+    getInstance().rnaHelices = null;
+  }
+
+  public static void initRnaHelicesShading(int n)
+  {
+    int i = 0;
+    ColourSchemes j = getInstance();
+
+    if (j.rnaHelices == null)
+    {
+      j.rnaHelices = new Color[n + 1];
+    }
+    else if (j.rnaHelices != null && j.rnaHelices.length <= n)
+    {
+      Color[] t = new Color[n + 1];
+      System.arraycopy(j.rnaHelices, 0, t, 0, j.rnaHelices.length);
+      i = j.rnaHelices.length;
+      j.rnaHelices = t;
+    }
+    else
+    {
+      return;
+    }
+    // Generate random colors and store
+    for (; i <= n; i++)
+    {
+      j.rnaHelices[i] = ColorUtils.generateRandomColor(Color.white);
+    }
+  }
+
+  /**
+   * a map from scheme name (lower-cased) to an instance of it
+   */
+  private Map<String, ColourSchemeI> schemes;
+
+  /**
    * Loads an instance of each standard or user-defined colour scheme
    * 
    * @return
@@ -45,17 +108,22 @@ 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 +146,7 @@ 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
@@ -96,16 +164,17 @@ public class ColourSchemes
   {
     if (name != null)
     {
-      schemes.remove(name.toLowerCase());
+      schemes.remove(name.toLowerCase(Locale.ROOT));
     }
   }
-  
+
   /**
    * Returns an instance of the colour scheme with which the given view may be
    * coloured
    * 
    * @param name
    *          name of the colour scheme
+   * @param viewport
    * @param forData
    *          the data to be coloured
    * @param optional
@@ -113,7 +182,7 @@ 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 +190,8 @@ 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 +207,7 @@ public class ColourSchemes
   public ColourSchemeI getColourScheme(String name,
           AnnotatedCollectionI forData)
   {
-    return getColourScheme(name, forData, null);
+    return getColourScheme(name, null, forData, null);
   }
 
   /**
@@ -165,6 +234,6 @@ public class ColourSchemes
     {
       return false;
     }
-    return schemes.containsKey(name.toLowerCase());
+    return schemes.containsKey(name.toLowerCase(Locale.ROOT));
   }
 }