From 79c34bea5d18899696e681e34eebd1c33fc1683b Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 29 Jan 2008 10:32:50 +0000 Subject: [PATCH] groovy from stdin --- help/html/features/clarguments.html | 2 +- help/html/features/groovy.html | 32 ++++++++++++++++++-------------- 2 files changed, 19 insertions(+), 15 deletions(-) diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html index 10917b4..8d6a4d8 100644 --- a/help/html/features/clarguments.html +++ b/help/html/features/clarguments.html @@ -108,7 +108,7 @@
-groovy FILE
-
Execute groovy script in FILE, after all other +
Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other arguments have been processed
diff --git a/help/html/features/groovy.html b/help/html/features/groovy.html index 1a0b83c..3e7b0f4 100644 --- a/help/html/features/groovy.html +++ b/help/html/features/groovy.html @@ -7,14 +7,28 @@ language for the Java platform". The groovy scripting language makes i 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.

-

Opening the Groovy Console
If groovy is available, then the +

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 linecommand line option will

-

There is as yet no properly defined scripting interface to Jalview, but all the +

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 @@ -30,16 +44,6 @@ def seq = alignment.getSequenceAt(0);

-

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.

 

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