+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
import jalview.workers.FeatureCounterI;
import jalview.workers.AlignmentAnnotationFactory;
* Example script that registers two alignment annotation calculators
* - one that counts residues in a column with Pfam annotation
* - one that counts only charged residues with Pfam annotation
- * To try this, first load uniref50.fa from the examples folder, then load features
- * from examples/exampleFeatures.txt, before running this script from the Groovy console.
+ *
+ * To try:
+ * 1. load uniref50.fa from the examples folder
+ * 2. load features onto it from from examples/exampleFeatures.txt
+ * 3. Open this script in the Groovy console.
+ * 4. Either execute this script from the console, or via Calculate->Run Groovy Script
- * Modify this example as required to count by column any desired value that can be
- * derived from the residue and sequence features at each position of an alignment.
+ * To explore further, try changing this script to count other kinds of occurrences of
+ * residue and sequence features at columns in an alignment.
*/
/*
}
/*
- * Closure that counts residues with a Pfam feature annotation
+ * Closure that computes an annotation based on
+ * presence of particular residues and features
* Parameters are
* - the name (label) for the alignment annotation
* - the description (tooltip) for the annotation
}
/*
- * Define an annotation that counts any residue with Pfam domain annotation
+ * Define an annotation row that counts any residue with Pfam domain annotation
*/
def pfamAnnotation = getColumnCounter("Pfam", "Count of residues with Pfam domain annotation", {true}, hasPfam)
/*
- * Define an annotation that counts charged residues with Pfam domain annotation
+ * Define an annotation row that counts charged residues with Pfam domain annotation
*/
def chargedPfamAnnotation = getColumnCounter("Pfam charged", "Count of charged residues with Pfam domain annotation", isCharged, hasPfam)