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;
52 public String getCalcName()
54 return "Conservation";
60 if ((alignViewport == null) || (calcMan == null)
61 || (alignViewport.isClosed()))
66 List<AlignmentAnnotation> ourAnnot = new ArrayList<>();
67 AlignmentI alignment = alignViewport.getAlignment();
68 conservation = alignViewport.getAlignmentConservationAnnotation();
69 quality = alignViewport.getAlignmentQualityAnnot();
70 ourAnnot.add(conservation);
71 ourAnnot.add(quality);
73 ConsPercGaps = alignViewport.getConsPercGaps();
74 // AlignViewport.UPDATING_CONSERVATION = true;
76 if (alignment == null || (alWidth = alignment.getWidth()) < 0)
78 // .updatingConservation = false;
79 // AlignViewport.UPDATING_CONSERVATION = false;
84 cons = Conservation.calculateConservation("All",
85 alignment.getSequences(), 0, alWidth - 1, false,
86 ConsPercGaps, quality != null);
87 } catch (IndexOutOfBoundsException x)
89 // probable race condition. just finish and return without any fuss.
92 updateResultAnnotation(true);
94 if ((alignViewport == null) || (calcMan == null)
95 || (alignViewport.isClosed()))
102 ap.paintAlignment(true, true);
107 private void updateResultAnnotation(boolean b)
109 if (b || !calcMan.isWorking(this) && cons != null
110 && conservation != null && quality != null)
112 alignViewport.setConservation(cons);
113 cons.completeAnnotations(conservation, quality, 0, alWidth);
118 public void updateAnnotation()
120 updateResultAnnotation(false);