/*
- * 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 2.8.1)
+ * 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.gui;
return;
}
- ColourSchemeI toChange = null;
- List<SequenceGroup> allGroups = null;
- int groupIndex = 0;
+ ColourSchemeI toChange = cs;
+ Iterator<SequenceGroup> allGroups = null;
if (allGroupsCheck.isSelected())
{
- allGroups = ap.av.getAlignment().getGroups();
- groupIndex = allGroups.size() - 1;
- }
- else
- {
- toChange = cs;
+ allGroups = ap.av.getAlignment().getGroups().listIterator();
}
- while (groupIndex > -1)
+ while (toChange != null)
{
- if (allGroups != null)
- {
- toChange = ((SequenceGroup) allGroups.get(groupIndex)).cs;
-
- if (toChange == null)
- {
- groupIndex--;
-
- continue;
- }
- }
-
if (forConservation)
{
- if (toChange.conservationApplied())
- {
- toChange.setConservationInc(i);
- }
+ toChange.setConservationInc(i);
}
else
{
toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
}
-
- groupIndex--;
+ if (allGroups != null && allGroups.hasNext())
+ {
+ while ((toChange = allGroups.next().cs) == null
+ && allGroups.hasNext())
+ ;
+ }
+ else
+ {
+ toChange = null;
+ }
}
ap.seqPanel.seqCanvas.repaint();