X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fgroovy.html;h=ead44369ef3f87aa2d19368b9056f2611a5880ac;hb=281aa090976818b388374b7aae780a29a8864b96;hp=a2bc627c3800e93f30b782d14fbd14096e6b8254;hpb=e8d85cb9e82777fa09359a8a6c02d80147105f0d;p=jalview.git diff --git a/help/html/features/groovy.html b/help/html/features/groovy.html index a2bc627..ead4436 100644 --- a/help/html/features/groovy.html +++ b/help/html/features/groovy.html @@ -27,21 +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 comes with
- an embedded installation of Groovy. All you need is to select Tools→Groovy
- Console... menu option 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 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
@@ -56,18 +58,30 @@
- Executing a groovy script on a particular alignment
-
-
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 environment 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
@@ -77,13 +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:
+