/*
- * 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 2.8.2)
+ * 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.workers;
-import java.util.ArrayList;
-import java.util.List;
-
import jalview.analysis.Conservation;
import jalview.api.AlignCalcWorkerI;
-import jalview.api.AlignmentViewPanel;
import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import java.util.ArrayList;
+import java.util.List;
+
public class ConservationThread extends AlignCalcWorker implements
AlignCalcWorkerI
{
if (alignViewport.isClosed())
{
abortAndDestroy();
+ return;
}
List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
AlignmentI alignment = alignViewport.getAlignment();
ourAnnot.add(conservation);
ourAnnot.add(quality);
ourAnnots = ourAnnot;
-
+ ConsPercGaps = alignViewport.getConsPercGaps();
// AlignViewport.UPDATING_CONSERVATION = true;
if (alignment == null || (alWidth = alignment.getWidth()) < 0)
{
if (b || !calcMan.isWorking(this) && cons != null
&& conservation != null && quality != null)
+ {
+ alignViewport.setConservation(cons);
cons.completeAnnotations(conservation, quality, 0, alWidth);
+ }
}
@Override