Groovy Shell

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fgroovy.html;fp=help%2Fhtml%2Ffeatures%2Fgroovy.html;h=adabdf15fe612bedb658b9265a184968e74f007f;hb=9623cea766a766683243235557ad48e6f7659e6a;hp=b49fc175866590771b359d5e183fe8f6cf429c77;hpb=6066400ed6b0fe288ebbea82389f59838a534706;p=jalview.git diff --git a/help/html/features/groovy.html b/help/html/features/groovy.html index b49fc17..adabdf1 100644 --- a/help/html/features/groovy.html +++ b/help/html/features/groovy.html @@ -23,75 +23,77 @@ 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 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. -

- 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
- 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();
+  
+    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 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.
+  
+  
+    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

+    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:
+  

+  
+    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);
-
-When running a groovy script from the command line, the alignment that was just loaded can be referred to like so:
+
+    
+    When running a groovy script from the command line, the
+      alignment that was just loaded can be referred to like so:

+     print currentAlFrame.getTitle();
-	
-	
-
-	 
+

+ If you have downloaded the InstallAnywhere version of Jalview, you can + find additional groovy scripts in the examples/groovy subfolder of the + installation directory.