From: gmungoc Date: Thu, 21 Apr 2016 09:56:53 +0000 (+0100) Subject: Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop X-Git-Tag: Release_2_10_0~249^2~17 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=49d07daba32cb7ca7841eca72c82cdf3c8d4344d;hp=35b237a7910f8b96b53938700cb427fb46e5e5af;p=jalview.git Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop --- diff --git a/.classpath b/.classpath index cad9e2b..4a3dbd6 100644 --- a/.classpath +++ b/.classpath @@ -39,7 +39,7 @@ - + diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS index c6c817a..caaa7f9 100644 --- a/THIRDPARTYLIBS +++ b/THIRDPARTYLIBS @@ -21,6 +21,7 @@ commons-discovery.jar commons-logging-1.1.1.jar commons-logging.jar commons-net-3.3.jar +groovy-all-2.4.6-indy.jar APL 2.0 License - downloaded and extracted from https://dl.bintray.com/groovy/maven/apache-groovy-binary-2.4.6.zip httpclient-4.0.3.jar httpcore-4.0.1.jar httpmime-4.0.3.jar diff --git a/doc/AddingGroovySupport.html b/doc/AddingGroovySupport.html index 41e34ce..63e7170 100644 --- a/doc/AddingGroovySupport.html +++ b/doc/AddingGroovySupport.html @@ -21,17 +21,10 @@

-Adding Groovy Support to Jalview +Groovy Support in Jalview

-There is currently no scripting language -extension within Jalview, in part because a -scripting API has not yet been developed. -

-

It is, however, really easy to embed scripting -engines like groovy. If groovy is detected on the -classpath, a new menu entry on the Desktop's Tools -menu will open the GroovyShell. + Groovy has been bundled with the Jalview desktop since circa 2012. The program supports interactive execution of groovy scripts via the Groovy Console, and command line execution via the '-groovy' option. The main source for documentation about Groovy in Jalview is the online help pages.

Here are some scripts to get you started:

  • Getting the title, alignment and first sequence from the current alignFrame
    @@ -43,13 +36,6 @@ def seq = alignment.getSequenceAt(0);
-

Getting Groovy...

-

-You need the core groovy jars which include the GroovyShell. The easiest way of doing -this is to add the groovy-all-*.jar to the lib directory whose path is given in the java.ext.dirs property.

-

The is obtained from the embedded directory within the groovy distribution). -

TODO

Using Java class methods from Groovy is straightforward, but currently, there isn't a set of easy to use methods for the jalview objects. A Jalview Scripting API needs to be developed to make this easier.

diff --git a/help/html/features/groovy.html b/help/html/features/groovy.html index adabdf1..9aa341b 100644 --- a/help/html/features/groovy.html +++ b/help/html/features/groovy.html @@ -27,7 +27,7 @@ The Groovy Shell

- Groovy is an "agile + 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 @@ -35,25 +35,12 @@ 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 + 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.

diff --git a/lib/groovy-all-1.8.2.jar b/lib/groovy-all-1.8.2.jar deleted file mode 100644 index 85af249..0000000 Binary files a/lib/groovy-all-1.8.2.jar and /dev/null differ diff --git a/lib/groovy-all-2.4.6-indy.jar b/lib/groovy-all-2.4.6-indy.jar new file mode 100644 index 0000000..5f3d51c Binary files /dev/null and b/lib/groovy-all-2.4.6-indy.jar differ diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index cb769bb..28ff0a1 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -4124,7 +4124,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { JMenuItem tm = new JMenuItem(); ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype); - if (sm.isProtein() == !viewport.getAlignment().isNucleotide()) + if (sm.isDNA() == viewport.getAlignment().isNucleotide() + || sm.isProtein() == !viewport.getAlignment() + .isNucleotide()) { String smn = MessageManager.getStringOrReturn( "label.score_model_", sm.getName()); diff --git a/utils/InstallAnywhere/Jalview.iap_xml b/utils/InstallAnywhere/Jalview.iap_xml index 83d1a98..428b998 100755 --- a/utils/InstallAnywhere/Jalview.iap_xml +++ b/utils/InstallAnywhere/Jalview.iap_xml @@ -2025,7 +2025,7 @@ and any path to a file to save to the file]]> - + false @@ -2043,7 +2043,7 @@ and any path to a file to save to the file]]> true - + 6149494