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 faada0e..18f24fb 100644 (file)
--- a/src/jalview/schemes/ColourSchemes.java
+++ b/src/jalview/schemes/ColourSchemes.java
@@ -23,24 +23,19 @@ 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
@@ -49,7 +44,8 @@ public class ColourSchemes
    */
   public static ColourSchemes getInstance()
   {
-    return instance;
+    return (ColourSchemes) ApplicationSingletonProvider
+            .getInstance(ColourSchemes.class);
   }
 
   private ColourSchemes()
@@ -58,6 +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
@@ -142,8 +183,8 @@ 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)
@@ -151,8 +192,7 @@ public class ColourSchemes
       return null;
     }
     ColourSchemeI cs = schemes.get(name.toLowerCase(Locale.ROOT));
-    return cs == null ? null
-            : cs.getInstance(viewport, forData);
+    return cs == null ? null : cs.getInstance(viewport, forData);
   }
 
   /**