From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 18 Jul 2016 15:29:34 +0000 (+0100)
Subject: JAL-2068 clearer instructions on how to use script (and modify it!)
X-Git-Tag: Release_2_10_0~138^2~2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4d5c8b2a59f1849d73d8c5784af6ae07fb5c6110;p=jalview.git

JAL-2068 clearer instructions on how to use script (and modify it!)
---

diff --git a/examples/groovy/featureCounter.groovy b/examples/groovy/featureCounter.groovy
index 3b5bca6..a16d8bb 100644
--- a/examples/groovy/featureCounter.groovy
+++ b/examples/groovy/featureCounter.groovy
@@ -5,11 +5,15 @@ 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.
  */
 
 /*