JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from...

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

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index fc92cd9..0123384 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -20,10 +20,8 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
-import jalview.util.ColorUtils;
-
-import java.awt.Color;
 
 /**
  * ColourSchemeProperty binds names to hardwired colourschemes and tries to deal
@@ -40,6 +38,11 @@ import java.awt.Color;
 public class ColourSchemeProperty
 {
 
+  private ColourSchemeProperty()
+  {
+    // requires static call to getColourScheme(...).
+  }
+
   /**
    * Returns a colour scheme for the given name, with which the given data may
    * be coloured. The name is not case-sensitive, and may be one of
@@ -75,7 +78,8 @@ public class ColourSchemeProperty
    * @param name
    * @return
    */
-  public static ColourSchemeI getColourScheme(AnnotatedCollectionI forData,
+  public static ColourSchemeI getColourScheme(AlignViewportI view,
+          AnnotatedCollectionI forData,
           String name)
   {
     if (ResidueColourScheme.NONE.equalsIgnoreCase(name))
@@ -89,6 +93,7 @@ public class ColourSchemeProperty
      * create a new instance of it
      */
     ColourSchemeI scheme = ColourSchemes.getInstance().getColourScheme(name,
+            view,
             forData, null);
     if (scheme != null)
     {
@@ -106,41 +111,6 @@ public class ColourSchemeProperty
     return ucs;
   }
 
-  public static Color rnaHelices[] = null;
-
-  public static void initRnaHelicesShading(int n)
-  {
-    int j = 0;
-    if (rnaHelices == null)
-    {
-      rnaHelices = new Color[n + 1];
-    }
-    else if (rnaHelices != null && rnaHelices.length <= n)
-    {
-      Color[] t = new Color[n + 1];
-      System.arraycopy(rnaHelices, 0, t, 0, rnaHelices.length);
-      j = rnaHelices.length;
-      rnaHelices = t;
-    }
-    else
-    {
-      return;
-    }
-    // Generate random colors and store
-    for (; j <= n; j++)
-    {
-      rnaHelices[j] = ColorUtils.generateRandomColor(Color.white);
-    }
-  }
-
-  /**
-   * delete the existing cached RNA helices colours
-   */
-  public static void resetRnaHelicesShading()
-  {
-    rnaHelices = null;
-  }
-
   /**
    * Returns the name of the colour scheme (or "None" if it is null)
    *