X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fgroovy.html;fp=help%2Fhtml%2Ffeatures%2Fgroovy.html;h=6db1d1c3ec548c5042511fc53e5e00e3d618cc98;hb=f06554784411ddbf871d642e66c8dcb7f147d4a8;hp=b49fc175866590771b359d5e183fe8f6cf429c77;hpb=cf06ee5d732af6cc874115aece1138adafca8ad7;p=jalview.git

diff --git a/help/html/features/groovy.html b/help/html/features/groovy.html
index b49fc17..6db1d1c 100644
--- a/help/html/features/groovy.html
+++ b/help/html/features/groovy.html
@@ -44,7 +44,7 @@
 		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
+		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>
@@ -59,13 +59,13 @@
 	</p>
 	<p>
 		<strong>Executing groovy scripts on Jalview startup</strong><br>
-		The -groovy &lt;script&gt; option on the <a href="commandline.html" />
+		The -groovy &lt;script&gt; option on the <a href="commandline.html">
 		Jalview command line</a> will execute the contents of &lt;script&gt;.
 		&lt;script&gt; may be a file, a URL, or alternatively if it is
 		&quot;STDIN&quot; then the standard input will be used.<br>
 		<em>Note: The groovy script will be executed <strong>after</strong>
 			any data is loaded, and <strong>before</strong> images or any output
-			files are written. This allows you to perform customised jalview
+			files are written. This allows you to perform customised Jalview
 			analysis workflows with groovy.</em>
 	</p>
 	<p>
@@ -76,13 +76,12 @@
 		object defined in the groovy environent which corresponds to the
 	<pre>jalview.gui.Desktop</pre>
 	object which manages all the Jalview windows.
-	</p>
 	Here's an example to get you started:
 	<br>
 	<ul>
 		<li>Getting the title, alignment and first sequence from the
 			current alignFrame<br> <pre>
-def alf = Jalview.getAlignframes();
+def alf = Jalview.getAlignFrames();
 print alf[0].getTitle();
 def alignment = alf[0].viewport.alignment;
 def seq = alignment.getSequenceAt(0);
@@ -90,8 +89,6 @@ def seq = alignment.getSequenceAt(0);
 <li>When running a groovy script from the command line, the alignment that was just loaded can be referred to like so:<br><pre>
 print currentAlFrame.getTitle();</pre>
 	</ul>
-	</p>
-
-	<p>&nbsp;</p>
+If you have downloaded the InstallAnywhere version of Jalview, you can find additional groovy scripts in the examples/groovy subfolder of the installation directory.
 </body>
 </html>