JAL-1807 explicit imports (jalview.schemes)

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

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 385e080..025a7a0 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -21,6 +21,7 @@
 package jalview.schemes;
 
 import jalview.datamodel.AnnotatedCollectionI;
+import jalview.util.ColorUtils;
 
 import java.awt.Color;
 
@@ -88,7 +89,7 @@ public class ColourSchemeProperty
   public static final int COVARIATION = 14;
 
   public static final int TCOFFEE = 15;
-  
+
   public static final int RNAHELIX = 16;
 
   public static final int RNAINTERACTION = 17;
@@ -352,11 +353,11 @@ public class ColourSchemeProperty
       ret = "T-Coffee Scores";
 
       break;
-      
+
     case RNAINTERACTION:
-        ret = "RNA Interaction type";
+      ret = "RNA Interaction type";
 
-        break;
+      break;
     case RNAHELIX:
       ret = "RNA Helices";
 
@@ -415,8 +416,7 @@ public class ColourSchemeProperty
         try
         {
           // fix the launchApp user defined coloursheme transfer bug
-          jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
-                  "white");
+          UserColourScheme ucs = new UserColourScheme("white");
           ucs.parseAppletParameter(name);
 
         } catch (Exception e)
@@ -442,8 +442,7 @@ public class ColourSchemeProperty
    * @return null or an instance of the colourscheme configured to colour given
    *         sequence set
    */
-  public static ColourSchemeI getColour(
-          jalview.datamodel.AnnotatedCollectionI coll, int index)
+  public static ColourSchemeI getColour(AnnotatedCollectionI coll, int index)
   {
     // TODO 3.0 2.8 refactor signature to take an alignmentI like container so
     // colourschemes based on annotation can be initialised
@@ -513,13 +512,13 @@ public class ColourSchemeProperty
     case TCOFFEE:
       cs = new TCoffeeColourScheme(coll);
       break;
-    
+
     case RNAHELIX:
       cs = new RNAHelicesColour(coll);
       break;
-      
-      // case COVARIATION:
-      // cs = new CovariationColourScheme(annotation);
+
+    // case COVARIATION:
+    // cs = new CovariationColourScheme(annotation);
     // break;
 
     case USER_DEFINED:
@@ -597,4 +596,32 @@ public class ColourSchemeProperty
 
     return col;
   }
+
+  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);
+    }
+  }
+
 }