Groovy Shell

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fgroovy.html;h=77888dd617a83663145ad537808395a930bd352c;hb=64274c2916a94b2d7776bd8a7175fc0ce5cf8890;hp=4b63c61ef0d32ab921a5bd5e811431332fe6a898;hpb=c53aeee9a688f68d64106a968876e542f701fbc6;p=jalview.git diff --git a/help/html/features/groovy.html b/help/html/features/groovy.html index 4b63c61..77888dd 100644 --- a/help/html/features/groovy.html +++ b/help/html/features/groovy.html @@ -1,7 +1,7 @@ -Groovy Shell +--> + +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
-

+	
+		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, 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();
 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:
```
+print currentAlFrame.getTitle();
```
+