Groovy Shell

From f52c6d390a8bbc118582f3ba3ca06170bf9d5e48 Mon Sep 17 00:00:00 2001 From: Ben Soares Date: Fri, 20 Oct 2023 18:17:04 +0100 Subject: [PATCH] JAL-4298 Update help docs to reflect Groovy changes --- examples/groovy/parseproperties.groovy | 3 +-- help/help/html/features/groovy.html | 37 ++++++++++++++++------------ help/help/html/groovy/featuresCounter.html | 2 +- resources/lang/Messages.properties | 4 +-- 4 files changed, 25 insertions(+), 21 deletions(-) diff --git a/examples/groovy/parseproperties.groovy b/examples/groovy/parseproperties.groovy index 322d5e2..ceec6d2 100644 --- a/examples/groovy/parseproperties.groovy +++ b/examples/groovy/parseproperties.groovy @@ -23,8 +23,7 @@ import jalview.datamodel.*; import jalview.gui.AlignFrame; import jalview.gui.AlignViewport; -def af = Jalview.getAlignFrames(); -def al = af[0].viewport.alignment; +def al = Jalview.getCurrentAlignFrame().viewport.alignment; ParseProperties pp = new ParseProperties(al); pp.getScoresFromDescription("Score", "ScanPS Raw Score", "([-0-9.+]+)", true); def sqs = al.getSequenceAt(0); 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);

Copy and paste it into the groovy script console
Load the example Feredoxin project (the one that opens by default when you first launched Jalview)
Select Calculations→Execute Groovy +
Select Calculations→Run Groovy Console Script from the alignment window's menu bar to run the script on the current view.

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index 70eeb95..129dd54 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -1246,8 +1246,8 @@ label.mapping_method = Sequence \u27f7 Structure mapping method status.cancelled_image_export_operation = Cancelled {0} export operation info.error_creating_file = Error creating {0} file exception.outofmemory_loading_mmcif_file = Out of memory loading mmCIF File -label.run_groovy = Run Groovy console script -label.run_groovy_tip = Run the script in the Groovy console over this alignment +label.run_groovy = Run Groovy Console Script +label.run_groovy_tip = Run the script in the Groovy Console over this alignment label.couldnt_run_groovy_script = Failed to run Groovy script label.uniprot_sequence_fetcher = UniProt Sequence Fetcher action.next_page= >> -- 1.7.10.2