2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 The Jalview Authors
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
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.workers;
23 import java.util.ArrayList;
24 import java.util.List;
26 import jalview.analysis.Conservation;
27 import jalview.api.AlignCalcWorkerI;
28 import jalview.api.AlignmentViewPanel;
29 import jalview.api.AlignViewportI;
30 import jalview.datamodel.AlignmentAnnotation;
31 import jalview.datamodel.AlignmentI;
33 public class ConservationThread extends AlignCalcWorker implements
37 private int ConsPercGaps = 25; // JBPNote : This should be a configurable
40 public ConservationThread(AlignViewportI alignViewport,
41 AlignmentViewPanel alignPanel)
43 super(alignViewport, alignPanel);
44 ConsPercGaps = alignViewport.getConsPercGaps();
47 private Conservation cons;
49 AlignmentAnnotation conservation, quality;
58 calcMan.notifyStart(this); // updatingConservation = true;
60 while (!calcMan.notifyWorking(this))
66 // ap.paintAlignment(false);
69 } catch (Exception ex)
74 if (alignViewport.isClosed())
78 List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
79 AlignmentI alignment = alignViewport.getAlignment();
80 conservation = alignViewport.getAlignmentConservationAnnotation();
81 quality = alignViewport.getAlignmentQualityAnnot();
82 ourAnnot.add(conservation);
83 ourAnnot.add(quality);
85 ConsPercGaps = alignViewport.getConsPercGaps();
86 // AlignViewport.UPDATING_CONSERVATION = true;
88 if (alignment == null || (alWidth = alignment.getWidth()) < 0)
90 calcMan.workerComplete(this);
91 // .updatingConservation = false;
92 // AlignViewport.UPDATING_CONSERVATION = false;
98 cons = Conservation.calculateConservation("All",
99 jalview.schemes.ResidueProperties.propHash, 3,
100 alignment.getSequences(), 0, alWidth - 1, false,
101 ConsPercGaps, quality != null);
102 } catch (IndexOutOfBoundsException x)
104 // probable race condition. just finish and return without any fuss.
105 calcMan.workerComplete(this);
108 updateResultAnnotation(true);
109 } catch (OutOfMemoryError error)
111 ap.raiseOOMWarning("calculating conservation", error);
112 calcMan.workerCannotRun(this);
113 // alignViewport.conservation = null;
114 // this.alignViewport.quality = null;
117 calcMan.workerComplete(this);
121 ap.paintAlignment(true);
126 private void updateResultAnnotation(boolean b)
128 if (b || !calcMan.isWorking(this) && cons != null
129 && conservation != null && quality != null)
131 alignViewport.setConservation(cons);
132 cons.completeAnnotations(conservation, quality, 0, alWidth);
137 public void updateAnnotation()
139 updateResultAnnotation(false);