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.api.AlignCalcManagerI;
24 import jalview.api.AlignCalcManagerI2;
25 import jalview.api.AlignCalcWorkerI;
26 import jalview.api.AlignViewportI;
27 import jalview.api.AlignmentViewPanel;
28 import jalview.datamodel.AlignmentAnnotation;
29 import jalview.datamodel.AlignmentI;
30 import jalview.datamodel.Annotation;
32 import java.util.List;
35 * Base class for alignment calculation workers
40 public abstract class AlignCalcWorker implements AlignCalcWorkerI
43 * manager and data source for calculations
45 protected AlignViewportI alignViewport;
47 protected AlignCalcManagerI2 calcMan;
49 protected AlignmentViewPanel ap;
51 protected List<AlignmentAnnotation> ourAnnots;
53 public AlignCalcWorker(AlignViewportI alignViewport,
54 AlignmentViewPanel alignPanel)
56 this.alignViewport = alignViewport;
57 calcMan = alignViewport.getCalcManager();
61 protected void abortAndDestroy()
65 calcMan.cancelWorker(this);
66 calcMan.removeWorker(this);
75 public boolean involves(AlignmentAnnotation i)
77 return ourAnnots != null && ourAnnots.contains(i);
81 * Permanently removes from the alignment all annotation rows managed by this
85 public void removeAnnotation()
87 if (ourAnnots != null && alignViewport != null)
89 AlignmentI alignment = alignViewport.getAlignment();
90 synchronized (ourAnnots)
92 for (AlignmentAnnotation aa : ourAnnots)
94 alignment.deleteAnnotation(aa, true);
101 // TODO: allow GUI to query workers associated with annotation to add items to
102 // annotation label panel popup menu
105 public boolean isDeletable()
111 * Calculate min and max values of annotations and set as graphMin, graphMax
112 * on the AlignmentAnnotation. This is needed because otherwise, well, bad
118 protected void setGraphMinMax(AlignmentAnnotation ann, Annotation[] anns)
120 // TODO feels like this belongs inside AlignmentAnnotation!
121 float max = Float.MIN_VALUE;
122 float min = Float.MAX_VALUE;
124 for (Annotation a : anns)
130 max = Math.max(max, val);
131 min = Math.min(min, val);
141 public AlignViewportI getAlignViewport()
143 return alignViewport;