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 import jalview.workers.FeatureSetCounterI
22 import jalview.workers.AlignmentAnnotationFactory
25 * Demonstration of FeatureSetCounterI
26 * compute annotation tracks counting number of displayed
27 * features of each type in each column
31 * discover features on the current view
34 def featuresDisp=Jalview.getCurrentAlignFrame().currentView.featuresDisplayed
35 if (featuresDisp == null) {
36 print 'Need at least one feature visible on alignment'
38 def visibleFeatures=featuresDisp.visibleFeatures.toList()
39 assert 'java.util.ArrayList' == visibleFeatures.class.name
42 * A closure that returns an array of features present
43 * for each feature type in visibleFeatures
44 * Argument 'features' will be a list of SequenceFeature
48 int[] obs = new int[visibleFeatures.size]
52 * Here we inspect the type of the sequence feature.
53 * You can also test sf.description, sf.score, sf.featureGroup,
54 * sf.strand, sf.phase, sf.begin, sf.end
55 * or sf.getValue(attributeName) for GFF 'column 9' properties
58 for (type in visibleFeatures)
60 if (type.equals(sf.type))
71 * Define something that counts each visible feature type
73 def columnSetCounter =
75 getNames: { visibleFeatures as String[] },
76 getDescriptions: { visibleFeatures as String[] },
77 getMinColour: { [0, 255, 255] as int[] }, // cyan
78 getMaxColour: { [0, 0, 255] as int[] }, // blue
83 ] as FeatureSetCounterI
86 * and register the counter
88 AlignmentAnnotationFactory.newCalculator(columnSetCounter)