/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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 <http://www.gnu.org/licenses/>.
+ * 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;
if (forConservation)
{
- label.setText(MessageManager.getString("label.enter_value_increase_conservation_visibility"));
+ label.setText(MessageManager
+ .getString("label.enter_value_increase_conservation_visibility"));
slider.setMinimum(0);
slider.setMaximum(100);
}
else
{
- label.setText(MessageManager.getString("label.enter_percentage_identity_above_which_colour_residues"));
+ label.setText(MessageManager
+ .getString("label.enter_percentage_identity_above_which_colour_residues"));
slider.setMinimum(0);
slider.setMaximum(100);
}
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();