From: Jim Procter Date: Thu, 22 Sep 2016 13:16:53 +0000 (+0100) Subject: JAL-2189 JAL-1812 JAL-2068 new groovy doc section and example featureCounter script X-Git-Tag: Release_2_10_0~39^2~12 X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=c8c1f2ab3fab93b92f444063ab522b5a82cf6aee JAL-2189 JAL-1812 JAL-2068 new groovy doc section and example featureCounter script --- diff --git a/examples/groovy/featureCounter.groovy b/examples/groovy/featureCounter.groovy index a16d8bb..9059dd0 100644 --- a/examples/groovy/featureCounter.groovy +++ b/examples/groovy/featureCounter.groovy @@ -1,3 +1,24 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ + import jalview.workers.FeatureCounterI; import jalview.workers.AlignmentAnnotationFactory; diff --git a/help/help.jhm b/help/help.jhm index 53b09e5..1760d43 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -130,6 +130,7 @@ + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index c4476fd..ed95a61 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -156,9 +156,11 @@ + + + - diff --git a/help/html/features/groovy.html b/help/html/features/groovy.html index a2bc627..079cf9e 100644 --- a/help/html/features/groovy.html +++ b/help/html/features/groovy.html @@ -27,21 +27,23 @@ 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. + 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. 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. + 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
@@ -56,18 +58,29 @@

- 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: -
+ 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 - this is bound to jalview.bin.Jalview.
    Useful + methods include: +
      +
    • Jalview.getAlignFrames() - returns a list of + jalview.gui.AlignFrame objects
      • +
    • Jalview.getCurrentAlignFrame() - returns the alignment + window which is currently being looked at by the user
      • +
    • +
  • currentAlFrame - this is only defined when + running a Groovy script via the -groovy command line argument. It + returns the first alignment window created after acting on the + other arguments passed on the command line.
    • +
+

+ A simple script

  • Getting the title, alignment and first sequence from the current alignFrame
    @@ -77,13 +90,26 @@ 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:
    - 
    +    
  • If you wanted to do the same thing from the command line, you can refer to
+      alignment that was just loaded with currentAlFrame:
    
+      
     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. +

+ 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 featureCounter.groovy + example for more information. +

+