/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* 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;
{
return;
}
-
- // This loop will find the first rna structure annotation by which to colour
- // the sequences.
- AlignmentAnnotation[] annotations = av.getAlignment().getAlignmentAnnotation();
- for (int i = 0; i < annotations.length; i++) {
-
- // is this a sensible way of determining type of annotation?
- if (annotations[i].getRNAStruc() != null) {
- currentAnnotation = annotations[i];
- break;
- }
- }
- if (currentAnnotation == null)
- {
- System.err.println("Jalview is about to try and colour by RNAHelices even"
- + " though there are no RNA secondary structure annotations present!");
- currentAnnotation = av.getAlignment().getAlignmentAnnotation()[0];// annotations.getSelectedIndex()];
- }
-
RNAHelicesColour rhc = null;
- rhc = new RNAHelicesColour(currentAnnotation);
+ rhc = new RNAHelicesColour(av.getAlignment());
av.setGlobalColourScheme(rhc);
continue;
}
- sg.cs = new RNAHelicesColour(currentAnnotation);
+ sg.cs = new RNAHelicesColour(sg);
}
}