X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Ffeatures%2Fgroovy.html;h=ead44369ef3f87aa2d19368b9056f2611a5880ac;hb=806c9dc4a3d841fe36e7d17ab45d783a9fc95f26;hp=515f38753f5a5523146cc583e1c5280f6fbabc0d;hpb=c17661b22323a66090ea91e04751aa17461b17c5;p=jalview.git diff --git a/help/html/features/groovy.html b/help/html/features/groovy.html index 515f387..ead4436 100644 --- a/help/html/features/groovy.html +++ b/help/html/features/groovy.html @@ -27,34 +27,23 @@ The Groovy Shell
- Groovy is an "agile - and dynamic language for the Java platform". The groovy - scripting language makes it extremely easy to programmatically - interact with Java programs, in much the same way that Javascript is - used to generate and interact with applets and other objects on the - page. + Groovy (www.groovy-lang.org) + is an "agile and dynamic language for the Java + platform". The groovy scripting language makes it extremely + easy to programmatically interact with Java programs, in much the + same way that Javascript is used to generate and interact with + applets and other objects on the page.
- Getting Groovy...
Jalview Groovy
- support is only possible if the core groovy jars which include the
- GroovyShell are present on the CLASSPATH when Jalview is started.
-
- The jars are obtained from the embedded directory within - the groovy - distribution. 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. -
-
- Opening Jalview's Groovy Console
If groovy
- is available, then the Tools→Groovy
- Console... menu entry will be available from the Jalview Desktop's
- drop-down menu. Selecting this will open the Groovy Console which allows you to interactively execute Groovy
- scripts within the Jalview run-time environment.
+ Getting Groovy...
Jalview comes with an embedded
+ installation of Groovy. Just select Tools→Groovy
+ Console... from the Jalview Desktop's drop-down menu. After a
+ short pause, you should then see the Groovy
+ Console appear. This allows you to interactively execute Groovy
+ scripts whilst Jalview is running. We've also provided a Calculations→Execute
+ Groovy Script button so you can execute the currently loaded
+ groovy script whilst viewing an alignment.
Executing groovy scripts on Jalview startup
@@ -70,14 +59,29 @@
Access to Jalview's functions from Groovy Scripts
- 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 Jalview
- object defined in the groovy environent which corresponds to the
-
jalview.gui.Desktop- object which manages all the Jalview windows. Here's an example to get - you started: -
jalview.bin.Jalview
.
+ A simple script
@@ -87,13 +91,35 @@ def alignment = alf[0].viewport.alignment; def seq = alignment.getSequenceAt(0);
+
print currentAlFrame.getTitle();
+ Example scripts
If you have downloaded the
+ InstallAnywhere version of Jalview, you can find additional groovy
+ scripts in the examples/groovy subfolder of the installation
+ directory. The examples are also available at http://www.jalview.org/examples/groovy.
+
+ Using Groovy to add new Alignment Calculations
We've
+ simplified the alignment analysis programming interface in Jalview
+ 2.10 to make it easy for you to add your own dynamic annotation
+ tracks with Groovy. Have a look at the featuresCounter.groovy
+ example for more information.
+
+ Creating custom colourschemes
+ You can create your own alignment colourschemes with a groovy script. We've provided two examples:
+