/*
- * 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.
- *
+ *
* 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;
boolean adjusting = false;
- public RNAHelicesColourChooser(AlignViewportI av, final AlignmentViewPanel ap)
+ public RNAHelicesColourChooser(AlignViewportI av,
+ final AlignmentViewPanel ap)
{
oldcs = av.getGlobalColourScheme();
if (av.getAlignment().getGroups() != null)
{
oldgroupColours = new Hashtable();
- for (SequenceGroup sg:ap.getAlignment().getGroups())
+ for (SequenceGroup sg : ap.getAlignment().getGroups())
{
if (sg.cs != null)
{
{
return;
}
-
- currentAnnotation = av.getAlignment().getAlignmentAnnotation()[0];// annotations.getSelectedIndex()];
-
RNAHelicesColour rhc = null;
- rhc = new RNAHelicesColour(currentAnnotation);
-
+ rhc = new RNAHelicesColour(av.getAlignment());
+
av.setGlobalColourScheme(rhc);
if (av.getAlignment().getGroups() != null)
{
- for (SequenceGroup sg:ap.getAlignment().getGroups())
+ for (SequenceGroup sg : ap.getAlignment().getGroups())
{
if (sg.cs == null)
{
continue;
}
- sg.cs = new RNAHelicesColour(currentAnnotation);
+ sg.cs = new RNAHelicesColour(sg);
}
}
av.setGlobalColourScheme(oldcs);
if (av.getAlignment().getGroups() != null)
{
- for (SequenceGroup sg:ap.getAlignment().getGroups())
+ for (SequenceGroup sg : ap.getAlignment().getGroups())
{
sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
}