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.AlignViewportI;
24 import jalview.api.AlignmentViewPanel;
25 import jalview.datamodel.AlignmentAnnotation;
26 import jalview.datamodel.AlignmentI;
27 import jalview.datamodel.Annotation;
28 import jalview.datamodel.SequenceFeature;
29 import jalview.datamodel.SequenceI;
30 import jalview.renderer.seqfeatures.FeatureRenderer;
31 import jalview.util.ColorUtils;
32 import jalview.util.Comparison;
34 import java.awt.Color;
35 import java.util.ArrayList;
36 import java.util.List;
39 * A class to compute an alignment annotation with column counts of any
40 * properties of interest of positions in an alignment. <br>
41 * This is designed to be extensible, by supplying to the constructor an object
42 * that computes a count for each residue position, based on the residue value
43 * and any sequence features at that position.
46 class ColumnCounterWorker extends AlignCalcWorker
48 FeatureCounterI counter;
51 * Constructor registers the annotation for the given alignment frame
56 public ColumnCounterWorker(AlignViewportI viewport,
57 AlignmentViewPanel panel, FeatureCounterI counter)
59 super(viewport, panel);
60 ourAnnots = new ArrayList<AlignmentAnnotation>();
61 this.counter = counter;
62 calcMan.registerWorker(this);
66 * method called under control of AlignCalcManager to recompute the annotation
67 * when the alignment changes
74 calcMan.notifyStart(this);
76 while (!calcMan.notifyWorking(this))
81 } catch (InterruptedException ex)
86 if (alignViewport.isClosed())
93 if (alignViewport.getAlignment() != null)
98 } catch (IndexOutOfBoundsException x)
100 // probable race condition. just finish and return without any fuss.
104 } catch (OutOfMemoryError error)
106 ap.raiseOOMWarning("calculating feature counts", error);
107 calcMan.disableWorker(this);
110 calcMan.workerComplete(this);
115 ap.adjustAnnotationHeight();
116 ap.paintAlignment(true);
122 * Scan each column of the alignment to calculate a count by feature type. Set
123 * the count as the value of the alignment annotation for that feature type.
125 void computeAnnotations()
127 FeatureRenderer fr = new FeatureRenderer(alignViewport);
128 // TODO use the commented out code once JAL-2075 is fixed
129 // to get adequate performance on genomic length sequence
130 AlignmentI alignment = alignViewport.getAlignment();
131 // AlignmentView alignmentView = alignViewport.getAlignmentView(false);
132 // AlignmentI alignment = alignmentView.getVisibleAlignment(' ');
134 // int width = alignmentView.getWidth();
135 int width = alignment.getWidth();
136 int height = alignment.getHeight();
137 int[] counts = new int[width];
140 for (int col = 0; col < width; col++)
143 for (int row = 0; row < height; row++)
145 count += countFeaturesAt(alignment, col, row, fr);
148 max = Math.max(count, max);
151 Annotation[] anns = new Annotation[width];
153 * add non-zero counts as annotations
155 for (int i = 0; i < counts.length; i++)
157 int count = counts[i];
160 Color color = ColorUtils.getGraduatedColour(count, 0, Color.cyan,
162 anns[i] = new Annotation(String.valueOf(count),
163 String.valueOf(count), '0', count, color);
168 * construct the annotation, save it and add it to the displayed alignment
170 AlignmentAnnotation ann = new AlignmentAnnotation(counter.getName(),
171 counter.getDescription(), anns);
172 ann.showAllColLabels = true;
173 ann.scaleColLabel = true;
174 ann.graph = AlignmentAnnotation.BAR_GRAPH;
176 alignViewport.getAlignment().addAnnotation(ann);
180 * Returns a count of any feature types present at the specified position of
188 int countFeaturesAt(AlignmentI alignment, int col, int row,
191 SequenceI seq = alignment.getSequenceAt(row);
196 if (col >= seq.getLength())
198 return 0;// sequence doesn't extend this far
200 char res = seq.getCharAt(col);
201 if (Comparison.isGap(res))
205 int pos = seq.findPosition(col);
208 * compute a count for any displayed features at residue
210 // NB have to adjust pos if using AlignmentView.getVisibleAlignment
212 List<SequenceFeature> features = fr.findFeaturesAtRes(seq, pos);
213 int count = this.counter.count(String.valueOf(res), features);
218 * Method called when the user changes display options that may affect how the
219 * annotation is rendered, but do not change its values. Currently no such
220 * options affect user-defined annotation, so this method does nothing.
223 public void updateAnnotation()
229 * Answers true to indicate that if this worker's annotation is deleted from
230 * the display, the worker should also be removed. This prevents it running
231 * and recreating the annotation when the alignment changes.
234 public boolean isDeletable()