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 alignment annotations with column counts for a set of
40 * properties of interest on positions in an alignment. <br>
41 * This is designed to be extensible, by supplying to the constructor an object
42 * that computes a vector of counts for each residue position, based on the
43 * residue and and sequence features at that position.
46 class ColumnCounterSetWorker extends AlignCalcWorker
48 FeatureSetCounterI counter;
51 * Constructor registers the annotation for the given alignment frame
56 public ColumnCounterSetWorker(AlignViewportI viewport,
57 AlignmentViewPanel panel, FeatureSetCounterI 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())
92 if (alignViewport.getAlignment() != null)
97 } catch (IndexOutOfBoundsException x)
99 // probable race condition. just finish and return without any fuss.
103 } catch (OutOfMemoryError error)
105 ap.raiseOOMWarning("calculating feature counts", error);
106 calcMan.disableWorker(this);
109 calcMan.workerComplete(this);
114 ap.adjustAnnotationHeight();
115 ap.paintAlignment(true);
121 * Scan each column of the alignment to calculate a count by feature type. Set
122 * the count as the value of the alignment annotation for that feature type.
124 void computeAnnotations()
126 FeatureRenderer fr = new FeatureRenderer(alignViewport);
127 // TODO use the commented out code once JAL-2075 is fixed
128 // to get adequate performance on genomic length sequence
129 AlignmentI alignment = alignViewport.getAlignment();
130 // AlignmentView alignmentView = alignViewport.getAlignmentView(false);
131 // AlignmentI alignment = alignmentView.getVisibleAlignment(' ');
133 int rows = counter.getNames().length;
135 int width = alignment.getWidth();
136 int height = alignment.getHeight();
137 int[][] counts = new int[width][rows];
138 int max[] = new int[rows];
139 for (int crow = 0; crow < rows; crow++)
143 for (int col = 0; col < width; col++)
145 int[] count = counts[col];
146 for (int crow = 0; crow < rows; crow++)
150 for (int row = 0; row < height; row++)
152 int[] colcount = countFeaturesAt(alignment, col, row, fr);
153 if (colcount != null)
155 for (int crow = 0; crow < rows; crow++)
157 count[crow] += colcount[crow];
162 for (int crow = 0; crow < rows; crow++)
164 max[crow] = Math.max(count[crow], max[crow]);
167 for (int anrow = 0; anrow < rows; anrow++)
169 Annotation[] anns = new Annotation[width];
171 * add non-zero counts as annotations
173 for (int i = 0; i < counts.length; i++)
175 int count = counts[i][anrow];
178 Color color = ColorUtils.getGraduatedColour(count, 0, Color.cyan,
179 max[anrow], Color.blue);
180 String str = String.valueOf(count);
181 anns[i] = new Annotation(str, str, '0', count, color);
186 * construct or update the annotation
188 AlignmentAnnotation ann = alignViewport.getAlignment()
189 .findOrCreateAnnotation(counter.getNames()[anrow],
190 counter.getDescriptions()[anrow], false, null,
192 ann.description = counter.getDescriptions()[anrow];
193 ann.showAllColLabels = true;
194 ann.scaleColLabel = true;
195 ann.graph = AlignmentAnnotation.BAR_GRAPH;
196 ann.annotations = anns;
197 setGraphMinMax(ann, anns);
198 ann.validateRangeAndDisplay();
199 if (!ourAnnots.contains(ann))
207 * Returns a count of any feature types present at the specified position of
215 int[] countFeaturesAt(AlignmentI alignment, int col, int row,
218 SequenceI seq = alignment.getSequenceAt(row);
223 if (col >= seq.getLength())
225 return null;// sequence doesn't extend this far
227 char res = seq.getCharAt(col);
228 if (Comparison.isGap(res))
232 int pos = seq.findPosition(col);
235 * compute a count for any displayed features at residue
237 // NB have to adjust pos if using AlignmentView.getVisibleAlignment
239 List<SequenceFeature> features = fr.findFeaturesAtRes(seq, pos);
240 int[] count = this.counter.count(String.valueOf(res), features);
245 * Method called when the user changes display options that may affect how the
246 * annotation is rendered, but do not change its values. Currently no such
247 * options affect user-defined annotation, so this method does nothing.
250 public void updateAnnotation()
256 * Answers true to indicate that if this worker's annotation is deleted from
257 * the display, the worker should also be removed. This prevents it running
258 * and recreating the annotation when the alignment changes.
261 public boolean isDeletable()