Groovy Shell

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fgroovy.html;fp=help%2Fhelp%2Fhtml%2Ffeatures%2Fgroovy.html;h=6b5c4c06891ba411ea09e8ae430ca97ccafc94a2;hb=b122ba188c2ffcbb302809bafc02058e355643ee;hp=cb0b10c667595dd0bcf46df282289943ec02c4fb;hpb=e91b3bef83f320e13c59ad5d21d69f0abf3d7507;p=jalview.git diff --git a/help/help/html/features/groovy.html b/help/help/html/features/groovy.html index cb0b10c..6b5c4c0 100644 --- a/help/help/html/features/groovy.html +++ b/help/help/html/features/groovy.html @@ -20,11 +20,11 @@ * The Jalview Authors are detailed in the 'AUTHORS' file. --> -Groovy Shell +Groovy Console

- The Groovy Shell + The Groovy Console

Groovy (www.groovy-lang.org) @@ -41,8 +41,8 @@ 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 + scripts whilst Jalview is running. We've also provided a Calculations→Run + Groovy Console Script button so you can execute the currently loaded groovy script whilst viewing an alignment.

@@ -63,31 +63,36 @@ 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 - this is bound to jalview.bin.groovy.JalviewObject providing access to the following useful + methods:
- 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.
currentAlFrame When used on the command line this refers to the current opened alignment. +
+ When used from the Groovy Console, it refers to the alignment that was in focus when the Groovy Console was opened. +
+ When a Groovy Console script is run from Calculate->Run Groovy Console Script, currentAlFrame us updated to that alignment.

+ If you specify a --groovy argument before an --open argument + then you should ensure your script doesn't refer to currentAlFrame. +

+ +

A simple script

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 al = Jalview.getCurrentAlignFrame();
+print al.getTitle();
+def alignment = al.viewport.alignment;
 def seq = alignment.getSequenceAt(0);