2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ 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 jalview.analysis.Conservation;
24 import jalview.api.AlignViewportI;
25 import jalview.api.AlignmentViewPanel;
26 import jalview.datamodel.AlignmentAnnotation;
27 import jalview.datamodel.AlignmentI;
29 import java.util.ArrayList;
30 import java.util.List;
32 public class ConservationThread extends AlignCalcWorker
35 private int ConsPercGaps = 25; // JBPNote : This should be a configurable
38 public ConservationThread(AlignViewportI alignViewport,
39 AlignmentViewPanel alignPanel)
41 super(alignViewport, alignPanel);
42 ConsPercGaps = alignViewport.getConsPercGaps();
45 private Conservation cons;
47 AlignmentAnnotation conservation, quality;
54 if ((alignViewport == null) || (calcMan == null)
55 || (alignViewport.isClosed()))
60 List<AlignmentAnnotation> ourAnnot = new ArrayList<>();
61 AlignmentI alignment = alignViewport.getAlignment();
62 conservation = alignViewport.getAlignmentConservationAnnotation();
63 quality = alignViewport.getAlignmentQualityAnnot();
64 ourAnnot.add(conservation);
65 ourAnnot.add(quality);
67 ConsPercGaps = alignViewport.getConsPercGaps();
68 // AlignViewport.UPDATING_CONSERVATION = true;
70 if (alignment == null || (alWidth = alignment.getWidth()) < 0)
72 // .updatingConservation = false;
73 // AlignViewport.UPDATING_CONSERVATION = false;
78 cons = Conservation.calculateConservation("All",
79 alignment.getSequences(), 0, alWidth - 1, false,
80 ConsPercGaps, quality != null);
81 } catch (IndexOutOfBoundsException x)
83 // probable race condition. just finish and return without any fuss.
86 updateResultAnnotation(true);
88 if ((alignViewport == null) || (calcMan == null)
89 || (alignViewport.isClosed()))
96 ap.paintAlignment(true, true);
101 private void updateResultAnnotation(boolean b)
103 if (b || !calcMan.isWorking(this) && cons != null
104 && conservation != null && quality != null)
106 alignViewport.setConservation(cons);
107 cons.completeAnnotations(conservation, quality, 0, alWidth);
112 public void updateAnnotation()
114 updateResultAnnotation(false);