* 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
- * 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 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
+
+ * 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
* - a closure (groovy function) that tests whether to include a residue
* - a closure that tests whether to increment count based on sequence features
*/
-def getColumnCounter = { name, desc, residueTester, featureCounter ->
+def getColumnCounter = { name, desc, acceptResidue, acceptFeatures ->
[
getName: { name },
getDescription: { desc },
count:
{ res, feats ->
def c = 0
- if (residueTester.call(res))
+ if (acceptResidue.call(res))
{
- if (featureCounter.call(feats))
+ if (acceptFeatures.call(feats))
{
c++
}
}
/*
- * Define 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 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)