X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fgroovy.html;h=6559fd1df19bf7b6486ff5fbe0b683ad4cbb6c13;hb=b528740d54b70ef784725aca3122eeceabcff8f9;hp=2b7a303edc382afa163abe521705606b59b822f2;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git diff --git a/help/html/features/groovy.html b/help/html/features/groovy.html index 2b7a303..6559fd1 100644 --- a/help/html/features/groovy.html +++ b/help/html/features/groovy.html @@ -1,67 +1,97 @@ - - -
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 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: +
+def alf = Jalview.getAlignframes(); +print alf[0].getTitle(); +def alignment = alf[0].viewport.alignment; +def seq = alignment.getSequenceAt(0); +
+print currentAlFrame.getTitle();+
+ +