X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FRNAHelicesColour.java;h=9c2ec3e9fa0e124b31ddbde9b185d0cdcc3312e0;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=4416bfdbe3c4baac42b13eaf8e77016b5dee89b7;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git

diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java
index 4416bfd..9c2ec3e 100644
--- a/src/jalview/schemes/RNAHelicesColour.java
+++ b/src/jalview/schemes/RNAHelicesColour.java
@@ -1,28 +1,34 @@
 /*
- * 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.
- * 
+ * 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;
 
-import java.awt.*;
-import java.util.Hashtable;
-
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 
+import java.awt.Color;
+import java.util.Hashtable;
+import java.util.Map;
+
 /**
  * Looks at the information computed from an RNA Stockholm format file on the
  * secondary structure of the alignment. Extracts the information on the
@@ -35,15 +41,10 @@ public class RNAHelicesColour extends ResidueColourScheme
 {
 
   /**
-   * Stores random colors generated for the number of helices
-   */
-  public Hashtable helixcolorhash = new Hashtable();
-
-  /**
    * Maps sequence positions to the RNA helix they belong to. Key: position,
-   * Value: helix
+   * Value: helix TODO: Revise or drop in favour of annotation position numbers
    */
-  public Hashtable positionsToHelix = new Hashtable();
+  public Hashtable<Integer, String> positionsToHelix = new Hashtable<Integer, String>();
 
   /**
    * Number of helices in the RNA secondary structure
@@ -59,20 +60,66 @@ public class RNAHelicesColour extends ResidueColourScheme
   {
     super(ResidueProperties.nucleotideIndex);
     this.annotation = annotation;
+    ColourSchemeProperty.resetRnaHelicesShading();
     refresh();
   }
 
+  public RNAHelicesColour(AnnotatedCollectionI alignment)
+  {
+    super(ResidueProperties.nucleotideIndex);
+    ColourSchemeProperty.resetRnaHelicesShading();
+    alignmentChanged(alignment, null);
+  }
+
+  /**
+   * clones colour settings and annotation row data
+   * 
+   * @param rnaHelicesColour
+   */
+  public RNAHelicesColour(RNAHelicesColour rnaHelicesColour)
+  {
+    super(ResidueProperties.nucleotideIndex);
+    annotation = rnaHelicesColour.annotation;
+    refresh();
+  }
+
+  @Override
+  public void alignmentChanged(AnnotatedCollectionI alignment,
+          Map<SequenceI, SequenceCollectionI> hiddenReps)
+  {
+
+    // This loop will find the first rna structure annotation by which to colour
+    // the sequences.
+    AlignmentAnnotation[] annotations = alignment.getAlignmentAnnotation();
+    for (int i = 0; i < annotations.length; i++)
+    {
+
+      // is this a sensible way of determining type of annotation?
+      if (annotations[i].visible && annotations[i].isRNA()
+              && annotations[i].isValidStruc())
+      {
+        annotation = annotations[i];
+        break;
+      }
+    }
+
+    refresh();
+
+  }
+
   private long lastrefresh = -1;
 
   public void refresh()
   {
-    if (lastrefresh != annotation._rnasecstr.hashCode()
-            && annotation.isValidStruc())
+
+    if (annotation != null
+            && ((annotation._rnasecstr == null || lastrefresh != annotation._rnasecstr
+                    .hashCode()) && annotation.isValidStruc()))
     {
       annotation.getRNAStruc();
       lastrefresh = annotation._rnasecstr.hashCode();
       numHelix = 0;
-      positionsToHelix = new Hashtable();
+      positionsToHelix = new Hashtable<Integer, String>();
 
       // Figure out number of helices
       // Length of rnasecstr is the number of pairs of positions that base pair
@@ -99,16 +146,7 @@ public class RNAHelicesColour extends ResidueColourScheme
         }
 
       }
-
-      // Generate random colors and store
-      for (int j = 0; j <= numHelix; j++)
-      {
-        if (!helixcolorhash.containsKey(Integer.toString(j)))
-        {
-          helixcolorhash.put(Integer.toString(j),
-                  jalview.util.ColorUtils.generateRandomColor(Color.white));
-        }
-      }
+      ColourSchemeProperty.initRnaHelicesShading(numHelix);
     }
   }
 
@@ -135,7 +173,7 @@ public class RNAHelicesColour extends ResidueColourScheme
    * @param c
    *          Character in sequence
    * @param j
-   *          Threshold
+   *          position in sequence - used to locate helix
    * 
    * @return Color in RGB
    */
@@ -145,15 +183,19 @@ public class RNAHelicesColour extends ResidueColourScheme
     refresh();
     Color currentColour = Color.white;
     String currentHelix = null;
-    currentHelix = (String) positionsToHelix.get(j);
-
+    currentHelix = positionsToHelix.get(j);
     if (currentHelix != null)
     {
-      currentColour = (Color) helixcolorhash.get(currentHelix);
+      currentColour = ColourSchemeProperty.rnaHelices[Integer
+              .parseInt(currentHelix)];
     }
-
-    // System.out.println(c + " " + j + " helix " + currentHelix + " " +
-    // currentColour);
     return currentColour;
   }
-}
+
+  @Override
+  public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+  {
+    return new RNAHelicesColour(this);
+  }
+}
\ No newline at end of file