import jalview.datamodel.AlignmentI;
/**
- * 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
}