2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.workers;
20 import jalview.analysis.Conservation;
21 import jalview.api.AlignCalcWorkerI;
22 import jalview.api.AlignmentViewPanel;
23 import jalview.api.AlignViewportI;
24 import jalview.datamodel.AlignmentAnnotation;
25 import jalview.datamodel.AlignmentI;
27 public class ConservationThread extends AlignCalcWorker implements AlignCalcWorkerI
30 private int ConsPercGaps = 25; // JBPNote : This should be a configurable property!
32 public ConservationThread(AlignViewportI alignViewport, AlignmentViewPanel alignPanel)
34 super(alignViewport, alignPanel);
35 ConsPercGaps = alignViewport.getConsPercGaps();
42 calcMan.notifyStart(this); // updatingConservation = true;
44 while (!calcMan.notifyWorking(this))
50 ap.paintAlignment(false);
53 } catch (Exception ex)
58 if (alignViewport.isClosed()) {
62 AlignmentI alignment=alignViewport.getAlignment();
63 AlignmentAnnotation conservation=alignViewport.getAlignmentConservationAnnotation();
64 AlignmentAnnotation quality=alignViewport.getAlignmentQualityAnnot();
65 // AlignViewport.UPDATING_CONSERVATION = true;
69 if (alignment==null || (alWidth=alignment.getWidth())< 0)
71 calcMan.workerComplete(this);
72 //.updatingConservation = false;
73 //AlignViewport.UPDATING_CONSERVATION = false;
78 Conservation cons = Conservation.calculateConservation("All",
79 jalview.schemes.ResidueProperties.propHash, 3,
80 alignment.getSequences(), 0, alWidth - 1, false, ConsPercGaps, quality!=null);
81 cons.completeAnnotations(conservation,
83 } catch (OutOfMemoryError error)
85 ap.raiseOOMWarning("calculating conservation", error);
86 calcMan.workerCannotRun(this);
87 // alignViewport.conservation = null;
88 // this.alignViewport.quality = null;
91 calcMan.workerComplete(this);
95 ap.paintAlignment(true);