<classpathentry kind="lib" path="lib/jdas-1.0.4.jar"/>
<classpathentry kind="lib" path="lib/spring-core-3.0.5.RELEASE.jar"/>
<classpathentry kind="lib" path="lib/spring-web-3.0.5.RELEASE.jar"/>
- <classpathentry kind="lib" path="lib/groovy-all-1.8.2.jar"/>
+ <classpathentry kind="lib" path="lib/groovy-all-2.4.6-indy.jar"/>
<classpathentry kind="lib" path="lib/min-jabaws-client-2.1.0.jar" sourcepath="/clustengine"/>
<classpathentry kind="lib" path="lib/json_simple-1.1.jar" sourcepath="/Users/jimp/Downloads/json_simple-1.1-all.zip"/>
<classpathentry kind="lib" path="lib/slf4j-api-1.7.7.jar"/>
commons-logging-1.1.1.jar
commons-logging.jar
commons-net-3.3.jar
+groovy-all-2.4.6-indy.jar APL 2.0 License - downloaded and extracted from https://dl.bintray.com/groovy/maven/apache-groovy-binary-2.4.6.zip
httpclient-4.0.3.jar
httpcore-4.0.1.jar
httpmime-4.0.3.jar
</title>
<body>
<h1>
-Adding Groovy Support to Jalview
+Groovy Support in Jalview
</h1>
<p>
-There is currently no scripting language
-extension within Jalview, in part because a
-scripting API has not yet been developed.
-</p>
-<p>It is, however, really easy to embed scripting
-engines like groovy. If groovy is detected on the
-classpath, a new menu entry on the Desktop's Tools
-menu will open the GroovyShell.
+ <a href="http://www.groovy-lang.org">Groovy</a> has been bundled with the Jalview desktop since circa 2012. The program supports interactive execution of groovy scripts via the Groovy Console, and command line execution via the '-groovy' option. The main source for documentation about Groovy in Jalview is the <a href="http://www.jalview.org/help/html/features/groovy.html">online help pages</a>.
</p>
<p>Here are some scripts to get you started:</p>
<ul><li>Getting the title, alignment and first sequence from the current alignFrame<br>
</pre>
</li>
</ul>
-<h1>Getting Groovy...</h1>
-<p>
-You need the core groovy jars which include the GroovyShell. The easiest way of doing
-this is to add the groovy-all-*.jar to the lib directory whose path is given in the java.ext.dirs property.</p>
-<p>The is obtained from the <em>embedded</em> directory within the <a
-href="http://dist.codehaus.org/groovy/distributions"/>groovy distribution</a>).
-</p>
<h2>TODO</h2>
<p>
Using Java class methods from Groovy is straightforward, but currently, there isn't a set of easy to use methods for the jalview objects. A Jalview Scripting API needs to be developed to make this easier.</p>
<strong>The Groovy Shell</strong>
</p>
<p>
- <a href="http://groovy.codehaus.org/">Groovy</a> is an "<em>agile
+ <a href="http://www.groovy-lang.org/">Groovy</a> is an "<em>agile
and dynamic language for the Java platform</em>". The groovy
scripting language makes it extremely easy to programmatically
interact with Java programs, in much the same way that Javascript is
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→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→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>
{
JMenuItem tm = new JMenuItem();
ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
- if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
+ if (sm.isDNA() == viewport.getAlignment().isNucleotide()
+ || sm.isProtein() == !viewport.getAlignment()
+ .isNucleotide())
{
String smn = MessageManager.getStringOrReturn(
"label.score_model_", sm.getName());
<string><![CDATA[664]]></string>
</property>
<property name="sourceName">
- <string><![CDATA[groovy-all-1.8.2.jar]]></string>
+ <string><![CDATA[groovy-all-2.4.6-indy.jar]]></string>
</property>
<property name="overrideUnixPermissions">
<boolean>false</boolean>
<boolean>true</boolean>
</property>
<property name="destinationName">
- <string><![CDATA[groovy-all-1.8.2.jar]]></string>
+ <string><![CDATA[groovy-all-2.4.6-indy.jar]]></string>
</property>
<property name="fileSize">
<long>6149494</long>
git://source.jalview.org / jalview.git / commitdiff