X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Ffeatures%2Fgroovy.html;h=ead44369ef3f87aa2d19368b9056f2611a5880ac;hb=c39137ea1057fea32d65471a12855a68d00365d5;hp=d9aa13fde57c90b578d0ed71687a80ec72c928ad;hpb=0696cffbccbb537be78d9fc2410589adbcd7be35;p=jalview.git diff --git a/help/html/features/groovy.html b/help/html/features/groovy.html index d9aa13f..ead4436 100644 --- a/help/html/features/groovy.html +++ b/help/html/features/groovy.html @@ -1,67 +1,125 @@ - - -
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 (www.groovy-lang.org) + 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. Just select Tools→Groovy
+ Console... 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 whilst Jalview is running. We've also provided a Calculations→Execute
+ Groovy Script button so you can execute the currently loaded
+ groovy script whilst viewing an alignment.
+
+ 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
+ The scripting interface to Jalview is still a work in progress, so
+ we recommend you also take a look at Jalview's source, since all the
+ public methods of the jalview class hierarchy can be called from
+ Groovy scripts. In addition, the following objects are also defined:
+
+
+
+
jalview.bin.Jalview
.
+ A simple script
+
+def alf = Jalview.getAlignFrames(); +print alf[0].getTitle(); +def alignment = alf[0].viewport.alignment; +def seq = alignment.getSequenceAt(0); ++
+print currentAlFrame.getTitle();+
+ Example scripts
If you have downloaded the
+ InstallAnywhere version of Jalview, you can find additional groovy
+ scripts in the examples/groovy subfolder of the installation
+ directory. The examples are also available at http://www.jalview.org/examples/groovy.
+
+ Using Groovy to add new Alignment Calculations
We've
+ simplified the alignment analysis programming interface in Jalview
+ 2.10 to make it easy for you to add your own dynamic annotation
+ tracks with Groovy. Have a look at the featuresCounter.groovy
+ example for more information.
+
+ Creating custom colourschemes
+ You can create your own alignment colourschemes with a groovy script. We've provided two examples:
+