X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fschemes%2FRNAHelicesColour.java;h=152ad9a333088907d9b450bc20e2dbae03c0ca36;hb=2ada5fb71ea7f372826f2f91cb4bfe33b4a4c660;hp=bfb760ec3e0bec36ba04be3bae884f0ad11ece18;hpb=9e16113678909f36fa3212c0fa7db1a61107ee5c;p=jalview.git
diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java
index bfb760e..152ad9a 100644
--- a/src/jalview/schemes/RNAHelicesColour.java
+++ b/src/jalview/schemes/RNAHelicesColour.java
@@ -1,26 +1,32 @@
/*
- * 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 2.8.2)
+ * 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.
- *
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * 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;
/**
@@ -62,11 +68,43 @@ public class RNAHelicesColour extends ResidueColourScheme
refresh();
}
+ public RNAHelicesColour(AnnotatedCollectionI alignment)
+ {
+ super(ResidueProperties.nucleotideIndex);
+ alignmentChanged(alignment, null);
+ }
+
+ @Override
+ public void alignmentChanged(AnnotatedCollectionI alignment,
+ Map 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].getRNAStruc() != null)
+ {
+ 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();