updated the Description of JAL-3798 - Jalview windows ocasionally dies when removing annotation rows.
changed the status to Being tested on JAL-2422 - Add support for linking Jalview with ChimeraX
feature/JAL-3690_callback-based-web-servicesin Chrome (doesn't start in Firefox at all) results in a following error:
TypeError: Cannot read property 'apply' of undefined TypeError: Cannot read property 'apply' of undefined at $I$ (swingjs/j2s/jalview/workers/AlignCalcManager2.js:1:475) at Object.eval [as getWorkers$] (swingjs/j2s/jalview/workers/AlignCalcManager2.js:25:8) at Object.eval [as getWorkersOfClass$Class] (swingjs/j2s/jalview/workers/AlignCalcManager2.js:30:33) at clazz.eval [as updateConservation$jalview_api_AlignmentViewPanel] (swingjs/j2s/jalview/viewmodel/AlignmentViewport.js:354:22) at clazz.eval [as addAlignmentPanel$jalview_gui_AlignmentPanel$Z] (swingjs/j2s/jalview/gui/AlignFrame.js:333:8) at clazz.eval [as c$$jalview_datamodel_AlignmentI$jalview_datamodel_HiddenColumns$I$I$S$S] (swingjs/j2s/jalview/gui/AlignFrame.js:43:6) at clazz.eval [as c$$jalview_datamodel_AlignmentI$jalview_datamodel_HiddenColumns$I$I$S] (swingjs/j2s/jalview/gui/AlignFrame.js:33:76) at clazz.eval [as c$$jalview_datamodel_AlignmentI$jalview_datamodel_HiddenColumns$I$I] (swingjs/j2s/jalview/gui/AlignFrame.js:29:74) at clazz.eval [as c$$jalview_datamodel_AlignmentI$I$I] (swingjs/j2s/jalview/gui/AlignFrame.js:17:72) at Object.Clazz.new_ (http://localhost:8000/swingjs/swingjs2.js:14562:19)
@BobHanson would it be possible to make the name/directory (even if relative) of the
.j2s file configurable (e.g. using a property)? I guess I'm looking at line 41 of https://github.com/java2script/java2script/blob/master/sources/net.sf.j2s.core/src/net/sf/j2s/core/Java2ScriptCompiler.java
private static final String J2S_OPTIONS_FILE_NAME = ".j2s";
and putting a static block in to look at property first. I could make up a PR if that would be easier?
I've updated the
develop branch with a slew of issues that went into the 126.96.36.199 release (see https://issues.jalview.org/browse/JAL-3775) along with the HTTPS and Authenticated proxy settings that didn't make it into 188.8.131.52 (see https://issues.jalview.org/browse/JAL-3633).
I've also (perhaps prematurely) added in the new
/resources/channel.props mechanism (see https://issues.jalview.org/browse/JAL-3594) which will allow for differently configured aspects of Jalview's appearance depending on the channel set (e.g. try
gradle getdown -PCHANNEL=DEVELOP -Pgetdown_appbase_override= java -jar ./getdown/files/11/getdown-launcher.jar ./getdown/files/11 jalview
I've made sure this also works with JalviewJS (thanks @BobHanson for making Class.getResource() does The Right Thing!) so you can build a JalviewJS with
gradle jalviewjs -PCHANNEL=JALVIEWJS gradle jalviewjsServer firefox ./jalviewjsTest.html
(you may need to configure
j2s.compiler.status = enable jalviewjs_eclipse_root = ~/buildtools/eclipse/jee-2020-03
in your local.properties for a headless build).
jalview.util.ChannelProperties provides a wrapper/helper for using the channel-specific items and is described in
ChannelProperties is the mechanism, and I've provided graphics for channels "DEVELOP", "RELEASE", "TEST-RELEASE" (not very different), "JALVIEWJS" and a default set also not very different from release. This includes the getdown splash screen and icons which are most different in DEVELOP. I'm quite pleased with the Jalview Develop splashscreen so have a go!
Pre-built Jalview Develop installers (these are bundled with the latest Java 11 runtime) can be found at http://www.jalview.org/getdown/install4j/develop/installers/11/ but these are not yet linked to from the website Development page. I'd intended to do that today but thought fixing the JalviewJS build on the develop branch was somewhat more important.
-Dlaf=metalto use Metal Look and Feel, but ...). The 18 days older version 11.0.9+11.1 does work. I suspect this will be the case for any distribution of OpenJDK, not just the AdoptOpenJDK one.
gradle jalviewjsbut just so you know: It's a two-stage setting -- you need a normal .j2s (which is what your Eclipse IDE will be using). It needs a property
j2s.config.altfilepropertyset to an arbitrary string. That arbitrary string is a property name that j2s will look for when it activates in Eclipse, and the value of that property is an alternative j2s config filename.
j2s.config.altfilepropertyset then gradle will add that particular property with a value "org.jalview.jalviewjsj2sfilename". When gradle runs eclipse headlessly it also sets the property "org.jalview.jalviewjsj2sfilename" to a different j2s filename (build/jalviewjs/config/j2s) which java2script in the headless Eclipse will then use.
6c27b7864 JAL-3789 New swingjs for Java2Script 3.2.10 with j2s.config.altfileproperty
dd81c1942 JAL-3789 Use j2s.config.altfileproperty in .j2s for alternative temporary build/jalviewjs/config/j2s settings file when running a headless build in gradle.