Groovy Shell

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fgroovy.html;h=bdaeab6b5295a8ca09fff73332133cbeb4f6e978;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=4f571dcd4bd758524e31bab58eb1eef7625a04c3;hpb=ab7509436f09413b122dace2ecd6692f6f06d347;p=jalview.git diff --git a/help/html/features/groovy.html b/help/html/features/groovy.html index 4f571dc..bdaeab6 100644 --- a/help/html/features/groovy.html +++ b/help/html/features/groovy.html @@ -1,94 +1,99 @@ - - - -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, 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();
```
-

- -

- - + + + +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();
+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. + +