X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Ffeatures%2Fgroovy.html;h=a2bc627c3800e93f30b782d14fbd14096e6b8254;hb=1f46c912a14d05f673e19b272fec4e6094874fa5;hp=d9aa13fde57c90b578d0ed71687a80ec72c928ad;hpb=0696cffbccbb537be78d9fc2410589adbcd7be35;p=jalview.git diff --git a/help/html/features/groovy.html b/help/html/features/groovy.html index d9aa13f..a2bc627 100644 --- a/help/html/features/groovy.html +++ b/help/html/features/groovy.html @@ -1,67 +1,89 @@ - - -
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.Desktopobject which -manages all the Jalview windows. -Here's an example to get you started:
-def alf = Jalview.getAlignframes(); -print alf[0].getTitle(); -def alignment = alf[0].viewport.alignment; -def seq = alignment.getSequenceAt(0); --
- - + + + +
+ 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.
+
+
+ Executing a groovy script on a particular alignment
+
+
+ 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: +
+def alf = Jalview.getAlignFrames(); +print alf[0].getTitle(); +def alignment = alf[0].viewport.alignment; +def seq = alignment.getSequenceAt(0); ++
+print currentAlFrame.getTitle();+