X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fgroovy.html;h=ead44369ef3f87aa2d19368b9056f2611a5880ac;hb=06beaa2f6eb56b94f4dd6408078a14e572cf0eb3;hp=66edaf9c3e5243d224a5ac331ba517768e2ebf4e;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git diff --git a/help/html/features/groovy.html b/help/html/features/groovy.html index 66edaf9..ead4436 100644 --- a/help/html/features/groovy.html +++ b/help/html/features/groovy.html @@ -1,18 +1,125 @@ - - + + +
++ The Groovy Shell +
++ 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. 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
+ The -groovy <script> option on the
+ Jalview command line will execute the contents of <script>.
+ <script> may be a file, a URL, or alternatively if it is
+ "STDIN" then the standard input will be used.
Note:
+ The groovy script will be executed after any data
+ is loaded, and before images or any output files
+ are written. This allows you to perform customised Jalview
+ analysis workflows with groovy.
+
+
+ Access to Jalview's functions from Groovy Scripts
+ The scripting interface to Jalview is still a work in progress, so
+ we recommend you also take a look at Jalview's source, since all the
+ public methods of the jalview class hierarchy can be called from
+ Groovy scripts. In addition, the following objects are also defined:
+
+
+
+
jalview.bin.Jalview
.
+ A simple script
+
+def alf = Jalview.getAlignFrames(); +print alf[0].getTitle(); +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:
+