Groovy Shell

X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fgroovy.html;h=66edaf9c3e5243d224a5ac331ba517768e2ebf4e;hp=30f3bb6056578d2df8859aa824d4780a664d54a6;hb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;hpb=247b4f59aad27b654fb55268b55645dc6496f12e diff --git a/help/html/features/groovy.html b/help/html/features/groovy.html index 30f3bb6..66edaf9 100644 --- a/help/html/features/groovy.html +++ b/help/html/features/groovy.html @@ -15,53 +15,4 @@ * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License along with Jalview. If not, see . ---!> -Groovy Shell - -

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.

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 -it's 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.

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, or alternatively if it is "STDIN" -then the standard input will be used.

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:
-

Getting the title, alignment and first sequence from the current alignFrame
-

-def alf = Jalview.getAlignframes();
-print alf[0].getTitle();
-def alignment = alf[0].viewport.alignment;
-def seq = alignment.getSequenceAt(0);
-

- -

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