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<>();
61 this.counter = counter;
62 calcMan.registerWorker(this);
66 public String getCalcName()
68 return "Column Counter Set";
72 * method called under control of AlignCalcManager to recompute the annotation
73 * when the alignment changes
78 boolean annotationAdded = false;
79 if (alignViewport.isClosed())
85 if (alignViewport.getAlignment() != null)
89 annotationAdded = computeAnnotations();
90 } catch (IndexOutOfBoundsException x)
92 // probable race condition. just finish and return without any fuss.
101 ap.adjustAnnotationHeight();
103 ap.paintAlignment(true, true);
109 * Scan each column of the alignment to calculate a count by feature type. Set
110 * the count as the value of the alignment annotation for that feature type.
114 boolean computeAnnotations()
116 FeatureRenderer fr = new FeatureRenderer(alignViewport);
117 // TODO use the commented out code once JAL-2075 is fixed
118 // to get adequate performance on genomic length sequence
119 AlignmentI alignment = alignViewport.getAlignment();
120 // AlignmentView alignmentView = alignViewport.getAlignmentView(false);
121 // AlignmentI alignment = alignmentView.getVisibleAlignment(' ');
123 int rows = counter.getNames().length;
125 int width = alignment.getWidth();
126 int height = alignment.getHeight();
127 int[][] counts = new int[width][rows];
128 int max[] = new int[rows];
129 for (int crow = 0; crow < rows; crow++)
134 int[] minC = counter.getMinColour();
135 int[] maxC = counter.getMaxColour();
136 Color minColour = new Color(minC[0], minC[1], minC[2]);
137 Color maxColour = new Color(maxC[0], maxC[1], maxC[2]);
139 for (int col = 0; col < width; col++)
141 int[] count = counts[col];
142 for (int crow = 0; crow < rows; crow++)
146 for (int row = 0; row < height; row++)
148 int[] colcount = countFeaturesAt(alignment, col, row, fr);
149 if (colcount != null)
151 for (int crow = 0; crow < rows; crow++)
153 count[crow] += colcount[crow];
158 for (int crow = 0; crow < rows; crow++)
160 max[crow] = Math.max(count[crow], max[crow]);
164 boolean annotationAdded = false;
166 for (int anrow = 0; anrow < rows; anrow++)
168 Annotation[] anns = new Annotation[width];
171 * add counts as annotations. zeros are needed since select-by-annotation ignores empty annotation positions
173 for (int i = 0; i < counts.length; i++)
175 int count = counts[i][anrow];
177 Color color = ColorUtils.getGraduatedColour(count, 0, minColour,
178 max[anrow], maxColour);
179 String str = String.valueOf(count);
180 anns[i] = new Annotation(str, str, '0', count, color);
181 rmax = Math.max(count, rmax);
185 * construct or update the annotation
187 String description = counter.getDescriptions()[anrow];
188 if (!alignment.findAnnotation(description).iterator().hasNext())
190 annotationAdded = true;
192 AlignmentAnnotation ann = alignment.findOrCreateAnnotation(
193 counter.getNames()[anrow], description, false, null, null);
194 ann.description = description;
195 ann.showAllColLabels = true;
196 ann.scaleColLabel = true;
197 ann.graph = AlignmentAnnotation.BAR_GRAPH;
198 ann.annotations = anns;
199 ann.graphMin = 0f; // minimum always zero count
200 ann.graphMax = rmax; // maximum count from loop over feature columns
201 ann.validateRangeAndDisplay();
202 if (!ourAnnots.contains(ann))
207 return annotationAdded;
211 * Returns a count of any feature types present at the specified position of
220 int[] countFeaturesAt(AlignmentI alignment, int col, int row,
223 SequenceI seq = alignment.getSequenceAt(row);
228 if (col >= seq.getLength())
230 return null;// sequence doesn't extend this far
232 char res = seq.getCharAt(col);
233 if (Comparison.isGap(res))
239 * compute a count for any displayed features at residue
242 List<SequenceFeature> features = fr.findFeaturesAtColumn(seq, col + 1);
243 int[] count = this.counter.count(String.valueOf(res), features);
248 * Method called when the user changes display options that may affect how the
249 * annotation is rendered, but do not change its values. Currently no such
250 * options affect user-defined annotation, so this method does nothing.
253 public void updateAnnotation()
259 * Answers true to indicate that if this worker's annotation is deleted from
260 * the display, the worker should also be removed. This prevents it running
261 * and recreating the annotation when the alignment changes.
264 public boolean isDeletable()