+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ */
+package jalview.workers;
+
+import jalview.analysis.Conservation;
+import jalview.api.AlignCalcWorkerI;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+
+public class ConservationThread extends AlignCalcWorker implements AlignCalcWorkerI
+{
+
+ private int ConsPercGaps = 25; // JBPNote : This should be a configurable property!
+
+ public ConservationThread(AlignViewportI alignViewport, AlignmentViewPanel alignPanel)
+ {
+ super(alignViewport, alignPanel);
+ ConsPercGaps = alignViewport.getConsPercGaps();
+ }
+
+ public void run()
+ {
+ try
+ {
+ calcMan.notifyStart(this); // updatingConservation = true;
+
+ while (calcMan.alreadyDoing(this)) //UPDATING_CONSERVATION)
+ {
+ try
+ {
+ if (ap != null)
+ {
+ ap.paintAlignment(false);
+ }
+ Thread.sleep(200);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ calcMan.notifyWorking(this);
+ if (alignViewport.isClosed()) {
+ abortAndDestroy();
+ }
+
+ AlignmentI alignment=alignViewport.getAlignment();
+ AlignmentAnnotation conservation=alignViewport.getAlignmentConservationAnnotation();
+ AlignmentAnnotation quality=alignViewport.getAlignmentQualityAnnot();
+ // AlignViewport.UPDATING_CONSERVATION = true;
+
+ int alWidth;
+
+ if (alignment==null || (alWidth=alignment.getWidth())< 0)
+ {
+ calcMan.workerComplete(this);
+ //.updatingConservation = false;
+ //AlignViewport.UPDATING_CONSERVATION = false;
+
+ return;
+ }
+
+ Conservation cons = Conservation.calculateConservation("All",
+ jalview.schemes.ResidueProperties.propHash, 3,
+ alignment.getSequences(), 0, alWidth - 1, false, ConsPercGaps, quality!=null);
+ cons.completeAnnotations(conservation,
+ quality, 0, alWidth);
+ } catch (OutOfMemoryError error)
+ {
+ ap.raiseOOMWarning("calculating conservation", error);
+ calcMan.workerCannotRun(this);
+ // alignViewport.conservation = null;
+ // this.alignViewport.quality = null;
+
+ }
+ calcMan.workerComplete(this);
+
+ if (ap != null)
+ {
+ ap.paintAlignment(true);
+ }
+
+ }
+}