-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.workers;
-import java.util.List;
-
import jalview.api.AlignCalcManagerI;
import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import java.util.List;
+
/**
- * Base class for alignment calculation workers
+ * Base class for alignment calculation workers
+ *
* @author jimp
- *
+ *
*/
public abstract class AlignCalcWorker implements AlignCalcWorkerI
{
* manager and data source for calculations
*/
protected AlignViewportI alignViewport;
+
protected AlignCalcManagerI calcMan;
+
protected AlignmentViewPanel ap;
- protected List<AlignmentAnnotation> ourAnnots=null;
-
+
+ protected List<AlignmentAnnotation> ourAnnots = null;
+
public AlignCalcWorker(AlignViewportI alignViewport,
AlignmentViewPanel alignPanel)
{
this.alignViewport = alignViewport;
- calcMan=alignViewport.getCalcManager();
- ap = alignPanel;
+ calcMan = alignViewport.getCalcManager();
+ ap = alignPanel;
}
+
protected void abortAndDestroy()
{
- if (calcMan!=null) {
+ if (calcMan != null)
+ {
calcMan.workerComplete(this);
}
- alignViewport=null;
- calcMan=null;
- ap=null;
-
+ alignViewport = null;
+ calcMan = null;
+ ap = null;
+
}
+
public boolean involves(AlignmentAnnotation i)
{
- return ourAnnots!=null && ourAnnots.contains(i);
+ return ourAnnots != null && ourAnnots.contains(i);
}
/**
- * permanently remove from the alignment all annotation rows managed by this worker
+ * permanently remove from the alignment all annotation rows managed by this
+ * worker
*/
@Override
public void removeOurAnnotation()
{
- if (ourAnnots!=null && alignViewport!=null)
+ if (ourAnnots != null && alignViewport != null)
{
- AlignmentI alignment=alignViewport.getAlignment();
- synchronized (ourAnnots) {
- for (AlignmentAnnotation aa:ourAnnots)
+ AlignmentI alignment = alignViewport.getAlignment();
+ synchronized (ourAnnots)
+ {
+ for (AlignmentAnnotation aa : ourAnnots)
{
alignment.deleteAnnotation(aa, true);
}
}
}
}
- // TODO: allow GUI to query workers associated with annotation to add items to annotation label panel popup menu
+ // TODO: allow GUI to query workers associated with annotation to add items to
+ // annotation label panel popup menu
}