merge from develop

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

diff --git a/help/html/features/groovy.html b/help/html/features/groovy.html
index b49fc17..6db1d1c 100644 (file)
--- 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>