Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

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

diff --git a/src/jalview/schemes/ColourSchemes.java b/src/jalview/schemes/ColourSchemes.java
index c3d0ea0..18f24fb 100644 (file)
--- a/src/jalview/schemes/ColourSchemes.java
+++ b/src/jalview/schemes/ColourSchemes.java
@@ -20,25 +20,22 @@
  */
 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
@@ -47,7 +44,8 @@ public class ColourSchemes
    */
   public static ColourSchemes getInstance()
   {
-    return instance;
+    return (ColourSchemes) ApplicationSingletonProvider
+            .getInstance(ColourSchemes.class);
   }
 
   private ColourSchemes()
@@ -56,6 +54,51 @@ 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
@@ -72,12 +115,16 @@ public class ColourSchemes
     {
       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();
       }
     }
   }
@@ -100,7 +147,7 @@ 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
@@ -118,7 +165,7 @@ public class ColourSchemes
   {
     if (name != null)
     {
-      schemes.remove(name.toLowerCase());
+      schemes.remove(name.toLowerCase(Locale.ROOT));
     }
   }
 
@@ -136,17 +183,16 @@ public class ColourSchemes
    *          represent
    * @return
    */
-  public ColourSchemeI getColourScheme(String name,
-          AlignViewportI viewport, AnnotatedCollectionI forData,
+  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, forData, hiddenRepSequences);
+    ColourSchemeI cs = schemes.get(name.toLowerCase(Locale.ROOT));
+    return cs == null ? null : cs.getInstance(viewport, forData);
   }
 
   /**
@@ -189,6 +235,6 @@ public class ColourSchemes
     {
       return false;
     }
-    return schemes.containsKey(name.toLowerCase());
+    return schemes.containsKey(name.toLowerCase(Locale.ROOT));
   }
 }