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.
22 import jalview.workers.FeatureSetCounterI;
23 import jalview.workers.AlignmentAnnotationFactory;
26 * Demonstration of FeatureSetWorker
27 * compute annotation tracks counting number of displayed
28 * features of each type in each column
32 * discover features on the current view
35 def featuresVis=jalview.bin.Jalview.currentAlignFrame.getCurrentView().getFeaturesDisplayed().getVisibleFeatures().toList();
36 assert 'java.util.ArrayList' == featuresVis.class.name
39 * A closure that returns a vector for featuresVis of 1 or 0 for any features of type observed
40 * Argument should be a list of SequenceFeature
42 def hasType = { features ->
43 int[] obs=new int[featuresVis.size()];
47 * Here we inspect the type of the sequence feature.
48 * You can also test sf.description, sf.score, sf.featureGroup,
49 * sf.strand, sf.phase, sf.begin, sf.end
50 * or sf.getValue(attributeName) for GFF 'column 9' properties
53 for (type in featuresVis) {
54 if (type.equals(sf.type)) {
66 * Closure to generate a counter for feature types in featuresVis
67 * calls hasType to count types in the int[] count(String res, List<SequenceFeature> feats) method
69 def getColumnSetCounter = {
71 getNames: { featuresVis as String[] },
72 getDescriptions: { featuresVis as String[] },
73 getMinColour: { [0, 255, 255] }, // cyan
74 getMaxColour: { [0, 0, 255] }, // blue
79 ] as FeatureSetCounterI }
82 * and register a FeatuerSetCounter instance
84 AlignmentAnnotationFactory.newCalculator(getColumnSetCounter.call())