From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 5 May 2016 14:36:08 +0000 (+0100)
Subject: JAL-2068 better documentation in example script
X-Git-Tag: Release_2_10_0~227^2~3
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c03875530f7e0ec66daf8b1273cb807b08454692;p=jalview.git

JAL-2068 better documentation in example script
---

diff --git a/examples/groovy/featureCounter.groovy b/examples/groovy/featureCounter.groovy
index 08d038d..42d3187 100644
--- a/examples/groovy/featureCounter.groovy
+++ b/examples/groovy/featureCounter.groovy
@@ -5,6 +5,9 @@ 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.
+ 
  * 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.
  */
@@ -49,7 +52,7 @@ def hasPfam = { features ->
  * - 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 },
@@ -58,9 +61,9 @@ def getColumnCounter = { name, desc, residueTester, featureCounter ->
      count: 
          { res, feats -> 
             def c = 0
-            if (residueTester.call(res))
+            if (acceptResidue.call(res))
             {
-                if (featureCounter.call(feats))
+                if (acceptFeatures.call(feats))
                 {
                     c++
                 }
@@ -71,12 +74,12 @@ def getColumnCounter = { name, desc, residueTester, featureCounter ->
 }
 
 /*
- * Define annotation that counts any residue with Pfam domain annotation
+ * Define an annotation 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 that counts charged residues with Pfam domain annotation
  */
 def chargedPfamAnnotation = getColumnCounter("Pfam charged", "Count of charged residues with Pfam domain annotation", isCharged, hasPfam)