JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 84b660f..500047b 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -1,19 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
+ * 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/>.
+ * 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;
@@ -86,17 +88,17 @@ 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 = 16;
+  public static final int RNAINTERACTION = 17;
 
   /**
    * index of first colourscheme (includes 'None')
    */
   public static final int FIRST_COLOUR = NONE;
 
-  public static final int LAST_COLOUR = RNAHELIX;
+  public static final int LAST_COLOUR = RNAINTERACTION;
 
   /**
    * DOCUMENT ME!
@@ -350,18 +352,15 @@ public class ColourSchemeProperty
       ret = "T-Coffee Scores";
 
       break;
-<<<<<<< HEAD
-      
+
     case RNAINTERACTION:
-        ret = "RNA Interaction type";
+      ret = "RNA Interaction type";
 
-        break;
-=======
+      break;
     case RNAHELIX:
       ret = "RNA Helices";
 
       break;
->>>>>>> JAL-952_rnahelix
     /*
      * case COVARIATION: ret = "Covariation";
      * 
@@ -514,13 +513,13 @@ 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:
@@ -598,4 +597,41 @@ 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] = jalview.util.ColorUtils
+              .generateRandomColor(Color.white);
+    }
+  }
+
+  /**
+   * delete the existing cached RNA helces colours
+   */
+  public static void resetRnaHelicesShading()
+  {
+    rnaHelices = null;
+  }
+
 }