JAL-1503 update version in GPL header

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

diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java
index 774fc95..0a37052 100644 (file)
--- a/src/jalview/schemes/RNAHelicesColour.java
+++ b/src/jalview/schemes/RNAHelicesColour.java
@@ -1,26 +1,31 @@
 /*
- * 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 2.8.1)
+ * Copyright (C) 2014 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 
  * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.schemes;
 
 import java.awt.*;
 import java.util.Hashtable;
+import java.util.Map;
 
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
 
 /**
  * Looks at the information computed from an RNA Stockholm format file on the
@@ -56,40 +61,86 @@ public class RNAHelicesColour extends ResidueColourScheme
    */
   public RNAHelicesColour(AlignmentAnnotation annotation)
   {
+    super(ResidueProperties.nucleotideIndex);
     this.annotation = annotation;
+    refresh();
+  }
+  public RNAHelicesColour(AnnotatedCollectionI alignment)
+  {
+    super(ResidueProperties.nucleotideIndex);
+    alignmentChanged(alignment, null);
+  }
 
-    // Figure out number of helices
-    // Length of rnasecstr is the number of pairs of positions that base pair
-    // with each other in the secondary structure
-    for (int x = 0; x < this.annotation._rnasecstr.length; x++)
-    {
+  @Override
+  public void alignmentChanged(AnnotatedCollectionI alignment,
+          Map<SequenceI, SequenceCollectionI> hiddenReps)
+  {
 
-      /*
-       * System.out.println(this.annotation._rnasecstr[x] + " Begin" +
-       * this.annotation._rnasecstr[x].getBegin());
-       */
-      // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
+    // 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].getRNAStruc() != null) { 
+                annotation = annotations[i];
+                break;
+        }
+    }
+
+    refresh();
 
-      positionsToHelix.put(this.annotation._rnasecstr[x].getBegin(),
-              this.annotation._rnasecstr[x].getFeatureGroup());
-      positionsToHelix.put(this.annotation._rnasecstr[x].getEnd(),
-              this.annotation._rnasecstr[x].getFeatureGroup());
+  }
+  private long lastrefresh = -1;
 
-      if (Integer.parseInt(this.annotation._rnasecstr[x].getFeatureGroup()) > numHelix)
+  public void refresh()
+  {
+    
+    if (annotation!=null && ((annotation._rnasecstr == null
+               || lastrefresh != annotation._rnasecstr.hashCode())
+            && annotation.isValidStruc()))
+    {
+      annotation.getRNAStruc();
+      lastrefresh = annotation._rnasecstr.hashCode();
+      numHelix = 0;
+      positionsToHelix = new Hashtable();
+
+      // Figure out number of helices
+      // Length of rnasecstr is the number of pairs of positions that base pair
+      // with each other in the secondary structure
+      for (int x = 0; x < this.annotation._rnasecstr.length; x++)
       {
-        numHelix = Integer.parseInt(this.annotation._rnasecstr[x]
-                .getFeatureGroup());
-      }
 
-    }
+        /*
+         * System.out.println(this.annotation._rnasecstr[x] + " Begin" +
+         * this.annotation._rnasecstr[x].getBegin());
+         */
+        // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
 
-    // Generate random colors and store
-    for (int j = 0; j <= numHelix; j++)
-    {
-      helixcolorhash.put(Integer.toString(j), jalview.util.ColorUtils
-              .generateRandomColor(Color.white));
-    }
+        positionsToHelix.put(this.annotation._rnasecstr[x].getBegin(),
+                this.annotation._rnasecstr[x].getFeatureGroup());
+        positionsToHelix.put(this.annotation._rnasecstr[x].getEnd(),
+                this.annotation._rnasecstr[x].getFeatureGroup());
+
+        if (Integer.parseInt(this.annotation._rnasecstr[x]
+                .getFeatureGroup()) > numHelix)
+        {
+          numHelix = Integer.parseInt(this.annotation._rnasecstr[x]
+                  .getFeatureGroup());
+        }
 
+      }
+
+      // 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));
+        }
+      }
+    }
   }
 
   /**
@@ -101,6 +152,7 @@ public class RNAHelicesColour extends ResidueColourScheme
    * 
    * @return color in RGB
    */
+  @Override
   public Color findColour(char c)
   {
     return ResidueProperties.purinepyrimidine[ResidueProperties.purinepyrimidineIndex[c]];
@@ -118,8 +170,10 @@ public class RNAHelicesColour extends ResidueColourScheme
    * 
    * @return Color in RGB
    */
-  public Color findColour(char c, int j)
+  @Override
+  public Color findColour(char c, int j, SequenceI seq)
   {
+    refresh();
     Color currentColour = Color.white;
     String currentHelix = null;
     currentHelix = (String) positionsToHelix.get(j);