Groovy Shell

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fgroovy.html;h=9aa341b0ccf17db48d50defb3c5d5b96addcbfa1;hb=c3e1c37990fa38644a76a1ac20f3fd21714ff49c;hp=d9aa13fde57c90b578d0ed71687a80ec72c928ad;hpb=0696cffbccbb537be78d9fc2410589adbcd7be35;p=jalview.git diff --git a/help/html/features/groovy.html b/help/html/features/groovy.html index d9aa13f..9aa341b 100644 --- a/help/html/features/groovy.html +++ b/help/html/features/groovy.html @@ -1,67 +1,86 @@ - - -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);
-

- -

- - + + + +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 comes with + an embedded installation of Groovy. All you need is to select Tools→Groovy + Console... menu option 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 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:
+
```
+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. + +