X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=500047b1e554a1423a4a6cfaf04872716aa8bb8d;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=1e2db769d4f445c30b54505380e9737678e5315c;hpb=3b5139b9b736abd652bcd00228a0e85fd8f85615;p=jalview.git

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 1e2db76..500047b 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -1,19 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ * 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.
- *
- * 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
+ * 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.
+ *  
+ * 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;
 
@@ -29,7 +32,7 @@ import java.awt.Color;
  * values of the colourscheme constants is important for callers of
  * getColourName(int i), since it can be used to enumerate the set of built in
  * colours. The FIRST_COLOUR and LAST_COLOUR symbols are provided for this.
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
@@ -86,20 +89,23 @@ public class ColourSchemeProperty
 
   public static final int TCOFFEE = 15;
 
+  public static final int RNAHELIX = 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 = NUCLEOTIDE;
+  public static final int LAST_COLOUR = RNAINTERACTION;
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param name
    *          DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public static int getColourIndexFromName(String name)
@@ -167,6 +173,14 @@ public class ColourSchemeProperty
     {
       ret = PURINEPYRIMIDINE;
     }
+    else if (name.equalsIgnoreCase("RNA Interaction type"))
+    {
+      ret = RNAINTERACTION;
+    }
+    else if (name.equalsIgnoreCase("RNA Helices"))
+    {
+      ret = RNAHELIX;
+    }
     // else if (name.equalsIgnoreCase("Covariation"))
     // {
     // ret = COVARIATION;
@@ -177,10 +191,10 @@ public class ColourSchemeProperty
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param cs
    *          DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public static String getColourName(ColourSchemeI cs)
@@ -240,6 +254,10 @@ public class ColourSchemeProperty
     {
       index = TCOFFEE;
     }
+    else if (cs instanceof RNAHelicesColour)
+    {
+      index = RNAHELIX;
+    }
     /*
      * else if (cs instanceof CovariationColourScheme) { index = COVARIATION; }
      */
@@ -259,10 +277,10 @@ public class ColourSchemeProperty
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param index
    *          DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public static String getColourName(int index)
@@ -334,9 +352,18 @@ public class ColourSchemeProperty
       ret = "T-Coffee Scores";
 
       break;
+
+    case RNAINTERACTION:
+      ret = "RNA Interaction type";
+
+      break;
+    case RNAHELIX:
+      ret = "RNA Helices";
+
+      break;
     /*
      * case COVARIATION: ret = "Covariation";
-     *
+     * 
      * break;
      */
     case USER_DEFINED:
@@ -352,9 +379,10 @@ public class ColourSchemeProperty
 
     return ret;
   }
+
   /**
    * retrieve or create colourscheme associated with name
-   *
+   * 
    * @param seqs
    *          sequences to colour
    * @param width
@@ -401,20 +429,24 @@ public class ColourSchemeProperty
   }
 
   /**
-   * Construct an instance of ColourSchemeI corresponding to the given colourscheme index
-   *
+   * Construct an instance of ColourSchemeI corresponding to the given
+   * colourscheme index
+   * 
    * @param seqs
    *          sequences to be coloured by colourscheme
    * @param width
    *          geometry of alignment
    * @param index
    *          colourscheme number
-   *
-   * @return null or an instance of the colourscheme configured to colour given sequence set
+   * 
+   * @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(
+          jalview.datamodel.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
+    // TODO 3.0 2.8 refactor signature to take an alignmentI like container so
+    // colourschemes based on annotation can be initialised
     ColourSchemeI cs = null;
 
     switch (index)
@@ -480,9 +512,14 @@ public class ColourSchemeProperty
 
     case TCOFFEE:
       cs = new TCoffeeColourScheme(coll);
+      break;
+
+    case RNAHELIX:
+      cs = new RNAHelicesColour(coll);
+      break;
+
     // case COVARIATION:
     // cs = new CovariationColourScheme(annotation);
-
     // break;
 
     case USER_DEFINED:
@@ -560,4 +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;
+  }
+
 }