Merge branch 'develop' into features/JAL-2094_colourInterface

[jalview.git] / help / html / features / groovy.html

diff --git a/help/html/features/groovy.html b/help/html/features/groovy.html
index 515f387..a2bc627 100644 (file)
--- a/help/html/features/groovy.html
+++ b/help/html/features/groovy.html
@@ -27,7 +27,7 @@
     <strong>The Groovy Shell</strong>
   </p>
   <p>
-    <a href="http://groovy.codehaus.org/">Groovy</a> is an &quot;<em>agile
+    <a href="http://www.groovy-lang.org/">Groovy</a> is an &quot;<em>agile
       and dynamic language for the Java platform</em>&quot;. The groovy
     scripting language makes it extremely easy to programmatically
     interact with Java programs, in much the same way that Javascript is
@@ -35,25 +35,12 @@
     page.
   </p>
   <p>
-    <strong><em>Getting Groovy...</em> </strong><br> Jalview Groovy
-    support is only possible if the core groovy jars which include the
-    GroovyShell are present on the CLASSPATH when Jalview is started.
-  </p>
-  <p>
-    The jars are obtained from the <em>embedded</em> directory within
-    the <a href="http://dist.codehaus.org/groovy/distributions">groovy
-      distribution</a>. The easiest way of adding them to the Jalview
-    classpath is to download and build Jalview from its source
-    distribution, and then add the groovy-all-*.jar to the lib directory
-    whose path is given in the java.ext.dirs property.
-  </p>
-  <p>
-    <strong>Opening Jalview's Groovy Console</strong><br>If groovy
-    is available, then the <strong>Tools&#8594;Groovy
-      Console...</strong> menu entry will be available from the Jalview Desktop's
-    drop-down menu. Selecting this will open the <a
-      href="http://groovy.codehaus.org/Groovy+Console"
-    >Groovy Console</a> which allows you to interactively execute Groovy
+    <strong><em>Getting Groovy...</em> </strong><br> Jalview comes with
+    an embedded installation of Groovy. All you need is to select <strong>Tools&#8594;Groovy
+      Console...</strong> menu option from the Jalview Desktop's
+    drop-down menu. After a short pause, you should then see the <a
+      href="http://groovy-lang.org/groovyconsole.html"
+    >Groovy Console</a> appear. This allows you to interactively execute Groovy
     scripts within the Jalview run-time environment.
   </p>
   <p>
@@ -69,11 +56,14 @@
     </em>
   </p>
   <p>
+    <strong>Executing a groovy script on a particular alignment</strong><br/>
+    
+  <p>
     <strong>Access to Jalview's functions from Groovy Scripts</strong><br>
     There is as yet no properly defined scripting interface to Jalview,
     but all the public methods of the jalview class hierarchy can be
     called from Groovy scripts. The access point for this is the <strong>Jalview</strong>
-    object defined in the groovy environent which corresponds to the
+    object defined in the groovy environment which corresponds to the
   <pre>jalview.gui.Desktop</pre>
   object which manages all the Jalview windows. Here's an example to get
   you started: