jalview.git
4 years agoJAL-3379 JalviewJS-API specs - preliminary
BobHanson [Sat, 6 Jun 2020 13:13:33 +0000 (08:13 -0500)]
JAL-3379 JalviewJS-API specs - preliminary

4 years agoJAL-3446 embedded file for proper name matching
BobHanson [Fri, 5 Jun 2020 22:09:46 +0000 (17:09 -0500)]
JAL-3446 embedded file for proper name matching

web app name "Jalview"

div id="Jalview-desktop-div"

So whatever name you give the applet must match the div tags.
Previously, the div name was associated with a different name,
Info.j2sAppID, or something like that. This is much more sensible.

Just don't name it "jalview", because that is a package name!

4 years agoJAL-3446 UrlDownloadClient and Test
BobHanson [Fri, 5 Jun 2020 21:46:09 +0000 (16:46 -0500)]
JAL-3446 UrlDownloadClient and Test

 - moving download to Platform
 - trivializing JavaScript method
 - expanding SwingJS to allow for nio methods

Note: SwingJS preserves byte[] in the File, Path, or FileOutputStream
objects as well as in J2S._javaFileCache. Because of that, one thing you
have to look out for is stale references. In this case, we have:

temp = new Path(...);
fos = new FileOutputStream(temp.toString);

now two independent pointers both refer to the tmp file.

rbc = new
   ReadableByteChannel(url.openStream());
fos.getChannel().transferFrom(rbc);

Now the bytes are in fos's channel, but they are not associated yet with
"tmp".

Files.copy(tmp, outfile);

This wasn't working in JavaScript, because Path tmp was out of date, and
so no bytes were being copied.

Working now, but still far to complicated for the simple operation of
transferring bytes from an InputStream to a File in JavaScript.

4 years agoJAL-3446 Desktop JS needs getIdentifiersOrgData();
BobHanson [Fri, 5 Jun 2020 16:33:19 +0000 (11:33 -0500)]
JAL-3446 Desktop JS needs       getIdentifiersOrgData();

4 years agoJAL-3446 forgot to escape Java in modified Platform.getAppID
BobHanson [Fri, 5 Jun 2020 15:35:23 +0000 (10:35 -0500)]
JAL-3446 forgot to escape Java in modified Platform.getAppID

4 years agoJAL-3446 new Locale("") moved to Platform for review.
BobHanson [Fri, 5 Jun 2020 15:22:33 +0000 (10:22 -0500)]
JAL-3446 new Locale("") moved to Platform for review.

4 years agoJAL-3446 AlignmentSorter/Test more documentation; bit cleaner code
BobHanson [Fri, 5 Jun 2020 14:30:55 +0000 (09:30 -0500)]
JAL-3446 AlignmentSorter/Test   more documentation; bit cleaner code

4 years agoJAL-3446 AlignmentSorter/Test fixed for instance
BobHanson [Fri, 5 Jun 2020 13:46:03 +0000 (08:46 -0500)]
JAL-3446 AlignmentSorter/Test fixed for instance

4 years agoJAL-3446 removes all JalviewJSApp dependency from jalview.bin.Jalview;
BobHanson [Fri, 5 Jun 2020 12:38:09 +0000 (07:38 -0500)]
JAL-3446 removes all JalviewJSApp dependency from jalview.bin.Jalview;
cleans up logic in Jalview.doMain

4 years agoMerge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into...
BobHanson [Fri, 5 Jun 2020 05:54:10 +0000 (00:54 -0500)]
Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop

4 years agoRefactoring of Jalview, JalviewAppLoader, JalviewApp, various
BobHanson [Fri, 5 Jun 2020 05:53:39 +0000 (00:53 -0500)]
Refactoring of Jalview, JalviewAppLoader, JalviewApp, various
applet-related interfaces

- makes JalviewJSApp the JavaScript interface "app" class
- removes JS interface from Jalview
- removes JalviewAppLoader and associated duplication of classes
- adds JavaScript selection and "oninit" listeners (untested)

4 years agoSwingJS upgrade for JSUtil and JSUtilI
BobHanson [Fri, 5 Jun 2020 05:51:07 +0000 (00:51 -0500)]
SwingJS upgrade for JSUtil and JSUtilI

4 years agoJAL-3446 new Jmol 15.1.3 jar
BobHanson [Fri, 5 Jun 2020 05:26:32 +0000 (00:26 -0500)]
JAL-3446 new Jmol 15.1.3 jar

- into j8lib

- removes netscape package dependence

4 years agoJAL-3225 Minor change to building.md for flexmark, and html output files from the...
Ben Soares [Thu, 4 Jun 2020 19:40:24 +0000 (20:40 +0100)]
JAL-3225 Minor change to building.md for flexmark, and html output files from the process, handy to have in repo for developers

4 years agoJAL-3225 Removed dependency on command line pandoc to convert .md files to .html...
Ben Soares [Thu, 4 Jun 2020 19:38:13 +0000 (20:38 +0100)]
JAL-3225 Removed dependency on command line pandoc to convert .md files to .html.  Now all files in doc/*.md will get converted to doc/*.html using flexmark within gradle process.

4 years agoJAL-1191 reduce logging level for warnings
gmungoc [Thu, 4 Jun 2020 16:22:29 +0000 (17:22 +0100)]
JAL-1191 reduce logging level for warnings

4 years agoJAL-3446 post-merge unit test fixes, formatting
gmungoc [Thu, 4 Jun 2020 16:21:29 +0000 (17:21 +0100)]
JAL-3446 post-merge unit test fixes, formatting

4 years agoI see...
BobHanson [Wed, 3 Jun 2020 21:30:49 +0000 (16:30 -0500)]
I see...

4 years agoadds link for __j2sflags.htm to template.html
BobHanson [Wed, 3 Jun 2020 21:30:12 +0000 (16:30 -0500)]
adds link for __j2sflags.htm to template.html

4 years agoupdated template.html
BobHanson [Wed, 3 Jun 2020 21:26:41 +0000 (16:26 -0500)]
updated template.html

4 years ago_jvjmol.txt
BobHanson [Wed, 3 Jun 2020 21:19:44 +0000 (16:19 -0500)]
_jvjmol.txt

4 years agoJAL-3664 support for new Locale(""), meaning "not actually a
BobHanson [Wed, 3 Jun 2020 20:54:57 +0000 (15:54 -0500)]
JAL-3664 support for new Locale(""), meaning "not actually a
ResourceBundle, just one file (MessageManager)

4 years agoJAL-3664 support for user.home, user.dir, user
BobHanson [Wed, 3 Jun 2020 20:54:03 +0000 (15:54 -0500)]
JAL-3664 support for user.home, user.dir, user

4 years agoJAL-3446 adds SIFTs JAL-3625 SiftsClient
BobHanson [Wed, 3 Jun 2020 20:47:30 +0000 (15:47 -0500)]
JAL-3446 adds SIFTs JAL-3625 SiftsClient

4 years agoJAL-3446 from JAL-3253 ApplicationSingletonProvider missing for
BobHanson [Wed, 3 Jun 2020 14:24:06 +0000 (09:24 -0500)]
JAL-3446 from JAL-3253 ApplicationSingletonProvider missing for
RestClient; others are just cosmetic

4 years agoJAL-3446 AsyncSwingWorker upgrade
BobHanson [Wed, 3 Jun 2020 13:12:37 +0000 (08:12 -0500)]
JAL-3446 AsyncSwingWorker upgrade

4 years agoJAL-3446 from JAL-3253 Discoverers
BobHanson [Wed, 3 Jun 2020 03:05:11 +0000 (22:05 -0500)]
JAL-3446 from JAL-3253 Discoverers

4 years agoJAL-3446 from JAL-3253 ApplicationSingletonProvider
BobHanson [Wed, 3 Jun 2020 00:58:05 +0000 (19:58 -0500)]
JAL-3446 from JAL-3253 ApplicationSingletonProvider
StructureSelectionManager and others

4 years agoJAL-3446 from JAL-3253 ApplicationSingletonProvider Desktop
BobHanson [Wed, 3 Jun 2020 00:29:28 +0000 (19:29 -0500)]
JAL-3446 from JAL-3253 ApplicationSingletonProvider Desktop

4 years agoJAL-3446 from JAL-3253 ApplicationSingletonProvider 1/many
BobHanson [Tue, 2 Jun 2020 23:47:20 +0000 (18:47 -0500)]
JAL-3446 from JAL-3253 ApplicationSingletonProvider 1/many

4 years agoJAL-3446 JAL-3401 from JAL-3253 HoldRepaint and SeqCanvas sizing issues.
BobHanson [Tue, 2 Jun 2020 23:23:42 +0000 (18:23 -0500)]
JAL-3446 JAL-3401 from JAL-3253 HoldRepaint and SeqCanvas sizing issues.

- integrated changes from 0b573ed (gmungoc)

4 years agoJAL-3446 from JAL-3253-applet Jalview2XML integration (retains
BobHanson [Tue, 2 Jun 2020 21:56:28 +0000 (16:56 -0500)]
JAL-3446 from JAL-3253-applet Jalview2XML integration (retains
GeneLocus; switches to invokeLater)

4 years agoJAL-3446 from JAL-3253-applet Desktop and Jws2Discoverer getInstance()
BobHanson [Tue, 2 Jun 2020 21:54:57 +0000 (16:54 -0500)]
JAL-3446 from JAL-3253-applet Desktop and Jws2Discoverer getInstance()

4 years agoJAL-3446 JAL-3401 from JAL-3253-applet AlignmentPanel.holdRepaint
BobHanson [Tue, 2 Jun 2020 21:51:32 +0000 (16:51 -0500)]
JAL-3446 JAL-3401 from JAL-3253-applet AlignmentPanel.holdRepaint

4 years agoJAL-3446 from JAL-3253 AppletFormatAdapter not fixed
BobHanson [Tue, 2 Jun 2020 21:06:05 +0000 (16:06 -0500)]
JAL-3446 from JAL-3253 AppletFormatAdapter not fixed

4 years agoPreferences/StructureViewer fix
BobHanson [Tue, 2 Jun 2020 21:04:47 +0000 (16:04 -0500)]
Preferences/StructureViewer fix

4 years agothis was supposed to go on a separate branch. Didn't know I had to be
BobHanson [Tue, 2 Jun 2020 18:22:59 +0000 (13:22 -0500)]
this was supposed to go on a separate branch. Didn't know I had to be
sure I was synchronized.

4 years agoMerge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into...
BobHanson [Tue, 2 Jun 2020 18:19:25 +0000 (13:19 -0500)]
Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop

4 years agoJAL-3446 JAL-3253 JAL-3445 BSML bbb XML format reader (preliminary)
BobHanson [Tue, 2 Jun 2020 17:28:18 +0000 (12:28 -0500)]
JAL-3446 JAL-3253 JAL-3445 BSML bbb XML format reader (preliminary)

4 years agoJAL-3225 some fixes to build.gradle for working in Eclipse and not always changing...
Ben Soares [Tue, 2 Jun 2020 16:30:51 +0000 (17:30 +0100)]
JAL-3225 some fixes to build.gradle for working in Eclipse and not always changing doc/building.html

4 years agoJAL-3446 JAL-3253 Preferences
BobHanson [Tue, 2 Jun 2020 15:20:30 +0000 (10:20 -0500)]
JAL-3446 JAL-3253 Preferences

- unnecessary static initialization of StructureViewer

4 years agoJAL-3446 from JAL-3253-applet StockholmFile updated to 26b115b (gmungoc)
BobHanson [Tue, 2 Jun 2020 12:27:43 +0000 (07:27 -0500)]
JAL-3446 from JAL-3253-applet StockholmFile updated to 26b115b (gmungoc)

4 years agohelpful hints from Ben
BobHanson [Tue, 2 Jun 2020 11:30:54 +0000 (06:30 -0500)]
helpful hints from Ben

4 years agoJAL-3446 latest jmol zip from JAL-3253-applet (commit c28e0a1)
gmungoc [Tue, 2 Jun 2020 10:19:16 +0000 (11:19 +0100)]
JAL-3446 latest jmol zip from JAL-3253-applet (commit c28e0a1)

4 years agoJAL-3446 fix broken test
gmungoc [Tue, 2 Jun 2020 10:00:36 +0000 (11:00 +0100)]
JAL-3446 fix broken test

4 years agoBob's gitignore addition
BobHanson [Tue, 2 Jun 2020 03:32:31 +0000 (22:32 -0500)]
Bob's gitignore addition

/build-site.xml
/buildcore.xml
/j11lib/intervalstore-v1.0.jar

4 years agoJAL-3626 from JAL-3253-applet Jalview.java
BobHanson [Tue, 2 Jun 2020 03:13:03 +0000 (22:13 -0500)]
JAL-3626 from JAL-3253-applet Jalview.java

adds JalviewLite interface; removes deprecated AppletContext interface

4 years agoJAL-3626 from JAL-3253-applet Cache applicationProperties made private
BobHanson [Tue, 2 Jun 2020 03:10:58 +0000 (22:10 -0500)]
JAL-3626 from JAL-3253-applet Cache applicationProperties made private

-- adds remove/setPropertyNoSave

4 years agoJAL-3626 from JAL-3253-applet Cache applicationProperties made private
BobHanson [Tue, 2 Jun 2020 00:34:02 +0000 (19:34 -0500)]
JAL-3626 from JAL-3253-applet Cache applicationProperties made private

-- adds remove/setPropertyNoSave

4 years agoJAL-3626 from JAL-3253-applet web page embedding
BobHanson [Tue, 2 Jun 2020 00:32:42 +0000 (19:32 -0500)]
JAL-3626 from JAL-3253-applet web page embedding

4 years agoJAL-3626 from JAL-3253-applet JalviewLite scrollTo capability
BobHanson [Mon, 1 Jun 2020 22:37:20 +0000 (17:37 -0500)]
JAL-3626 from JAL-3253-applet JalviewLite scrollTo capability

4 years agoJAL-3626 from JAL-3253-applet CalculationChooser
BobHanson [Mon, 1 Jun 2020 22:25:24 +0000 (17:25 -0500)]
JAL-3626 from JAL-3253-applet CalculationChooser

-- dissociated from panel for static access by JavaScript

4 years agoJAL-3626 from JAL-3253-applet StructureViewer/Chooser
BobHanson [Mon, 1 Jun 2020 22:18:07 +0000 (17:18 -0500)]
JAL-3626 from JAL-3253-applet StructureViewer/Chooser

-- disassociates viewer launch from chooser
-- for JavaScript interface

(sorry about JAL-3262 ref previously)

4 years agoJAL-3262 from JAL-3253-applet temp. Desktop instance hack
BobHanson [Mon, 1 Jun 2020 21:48:12 +0000 (16:48 -0500)]
JAL-3262 from JAL-3253-applet temp. Desktop instance hack

4 years agoJAL-3262 from JAL-3253-applet JalviewApp integration
BobHanson [Mon, 1 Jun 2020 21:43:44 +0000 (16:43 -0500)]
JAL-3262 from JAL-3253-applet JalviewApp integration

4 years agoJAL-3262 from JAL-3253-applet JalviewApp integration
BobHanson [Mon, 1 Jun 2020 21:41:54 +0000 (16:41 -0500)]
JAL-3262 from JAL-3253-applet JalviewApp integration

4 years agoJAL-3262 from JAL-3253-applet AppletParams + Cache.setPropertyNoSave
BobHanson [Mon, 1 Jun 2020 21:39:06 +0000 (16:39 -0500)]
JAL-3262 from JAL-3253-applet AppletParams + Cache.setPropertyNoSave

4 years agoJAL-3262 from JAL-3253-applet ArgsParser
BobHanson [Mon, 1 Jun 2020 21:33:54 +0000 (16:33 -0500)]
JAL-3262 from JAL-3253-applet ArgsParser

4 years agoJAL-3262 from JAL-3253-applet Platform JS interface upgrade
BobHanson [Mon, 1 Jun 2020 21:29:54 +0000 (16:29 -0500)]
JAL-3262 from JAL-3253-applet Platform JS interface upgrade

4 years agoJAL-3262 from JAL-3253-applet Preferences final static String upgrade
BobHanson [Mon, 1 Jun 2020 21:29:10 +0000 (16:29 -0500)]
JAL-3262 from JAL-3253-applet Preferences final static String upgrade

4 years agoJAL-3262 from JAL-3523-applet JalviewApp and JalviewJSApi
BobHanson [Mon, 1 Jun 2020 21:20:28 +0000 (16:20 -0500)]
JAL-3262 from JAL-3523-applet JalviewApp and JalviewJSApi

 - removes JaliewJSLite dependence
 - removes AlignFrameI reference

4 years agoJAL-3262 from JAL3253-applet core_jvjmol.z.js static load
BobHanson [Mon, 1 Jun 2020 21:14:33 +0000 (16:14 -0500)]
JAL-3262 from JAL3253-applet core_jvjmol.z.js static load

4 years agoJAL-3626 Regex optimization from JAL-3253-applet; also minor
BobHanson [Mon, 1 Jun 2020 21:10:28 +0000 (16:10 -0500)]
JAL-3626 Regex optimization from JAL-3253-applet; also minor
StockholmFile for loop opt.

4 years agoTHIRDPARTYLIBS referred to intervalstore-v1.0 still
BobHanson [Mon, 1 Jun 2020 19:22:56 +0000 (14:22 -0500)]
THIRDPARTYLIBS referred to intervalstore-v1.0 still

4 years agocorrects Platform.openURL
BobHanson [Mon, 1 Jun 2020 19:12:41 +0000 (14:12 -0500)]
corrects Platform.openURL

4 years agoJAL-3626 adding compatible Platform.java
BobHanson [Mon, 1 Jun 2020 19:02:47 +0000 (14:02 -0500)]
JAL-3626 adding compatible Platform.java

4 years agoSwingJS update
BobHanson [Mon, 1 Jun 2020 17:40:31 +0000 (12:40 -0500)]
SwingJS update

4 years agoMerge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into...
BobHanson [Mon, 1 Jun 2020 17:38:02 +0000 (12:38 -0500)]
Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop

4 years agoswingjs/api, javajs/async
BobHanson [Mon, 1 Jun 2020 17:32:19 +0000 (12:32 -0500)]
swingjs/api, javajs/async

4 years agoJAL-3225 small fixes for building within Eclipse
soares [Mon, 1 Jun 2020 14:54:16 +0000 (15:54 +0100)]
JAL-3225 small fixes for building within Eclipse

4 years agoMerge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview into...
soares [Thu, 28 May 2020 21:07:28 +0000 (22:07 +0100)]
Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview into Jalview-JS/develop

4 years agoJAL-3626 transpiler and SwingJS upgrade
BobHanson [Thu, 28 May 2020 20:58:58 +0000 (15:58 -0500)]
JAL-3626 transpiler and SwingJS upgrade

4 years agoVarna fix for hashtable.remove(value) [unclear]
BobHanson [Thu, 28 May 2020 20:58:09 +0000 (15:58 -0500)]
Varna fix for hashtable.remove(value) [unclear]

4 years agoJAL-3636 ColorUtils cleaner test for hex color
BobHanson [Thu, 28 May 2020 20:56:38 +0000 (15:56 -0500)]
JAL-3636 ColorUtils cleaner test for hex color

4 years agoMerge branch 'develop' into Jalview-JS/develop
soares [Thu, 28 May 2020 16:24:09 +0000 (17:24 +0100)]
Merge branch 'develop' into Jalview-JS/develop

4 years agoGitter comment 2020.05.28 Cache.log.err(msg) not appearing
BobHanson [Thu, 28 May 2020 13:39:29 +0000 (08:39 -0500)]
Gitter comment 2020.05.28 Cache.log.err(msg) not appearing

4 years agoJAL-3463 avoid Thread.sleep() as not supported in SwingJS
gmungoc [Mon, 18 May 2020 15:01:54 +0000 (16:01 +0100)]
JAL-3463 avoid Thread.sleep() as not supported in SwingJS

4 years agoJAL-3624 use temp file for SIFT download in JS, correct unmarshalling
gmungoc [Tue, 19 May 2020 10:50:41 +0000 (11:50 +0100)]
JAL-3624 use temp file for SIFT download in JS, correct unmarshalling

4 years agoJAL-3624 log when SIFTS mapping fails
gmungoc [Tue, 26 May 2020 13:21:49 +0000 (14:21 +0100)]
JAL-3624 log when SIFTS mapping fails

4 years agoJAL-3541 ensure deletion of cloverReportDir
Ben Soares [Wed, 27 May 2020 16:37:12 +0000 (17:37 +0100)]
JAL-3541 ensure deletion of cloverReportDir

4 years agoJAL-3541 small fix for clover.xml location expected by build server plugin, and comme...
Ben Soares [Wed, 27 May 2020 15:53:40 +0000 (16:53 +0100)]
JAL-3541 small fix for clover.xml location expected by build server plugin, and comment clarity

4 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Tue, 26 May 2020 16:27:08 +0000 (17:27 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

4 years agoJAL-1889 disable test failing on build server
gmungoc [Tue, 26 May 2020 16:26:55 +0000 (17:26 +0100)]
JAL-1889 disable test failing on build server

4 years agoMerge branch 'bug/JAL-3541_cloverReport_gradle_task_fails' into develop
soares [Tue, 26 May 2020 14:36:27 +0000 (15:36 +0100)]
Merge branch 'bug/JAL-3541_cloverReport_gradle_task_fails' into develop

4 years agoJAL-3541 added a property/variable style comment to build.gradle bug/JAL-3541_cloverReport_gradle_task_fails
soares [Tue, 26 May 2020 14:08:17 +0000 (15:08 +0100)]
JAL-3541 added a property/variable style comment to build.gradle

4 years agoJAL-3624 log when SIFTS mapping fails
gmungoc [Tue, 26 May 2020 13:21:49 +0000 (14:21 +0100)]
JAL-3624 log when SIFTS mapping fails

4 years agoMerge branch 'feature/JAL-3624siftsInJS' into develop
gmungoc [Tue, 26 May 2020 12:38:55 +0000 (13:38 +0100)]
Merge branch 'feature/JAL-3624siftsInJS' into develop

4 years agoJAL-3541 selectively merged build.gradle and gradle.properties
soares [Mon, 25 May 2020 23:14:15 +0000 (00:14 +0100)]
JAL-3541 selectively merged build.gradle and gradle.properties

4 years agoJAL-3626 rescue automatic configuration of JALVIEW_VERSION from the RELEASE propertie...
Jim Procter [Mon, 25 May 2020 13:33:39 +0000 (14:33 +0100)]
JAL-3626 rescue automatic configuration of JALVIEW_VERSION from the RELEASE properties file, and exclusion of ‘examples’ from the windows installer.


4 years agoJAL-3621 corrected sequence feature sort and test
gmungoc [Tue, 19 May 2020 17:27:40 +0000 (18:27 +0100)]
JAL-3621 corrected sequence feature sort and test

4 years agoJAL-3624 use temp file for SIFT download in JS, correct unmarshalling feature/JAL-3624siftsInJS
gmungoc [Tue, 19 May 2020 10:50:41 +0000 (11:50 +0100)]
JAL-3624 use temp file for SIFT download in JS, correct unmarshalling

4 years agoJAL-3463 avoid Thread.sleep() as not supported in SwingJS
gmungoc [Mon, 18 May 2020 15:01:54 +0000 (16:01 +0100)]
JAL-3463 avoid Thread.sleep() as not supported in SwingJS

4 years agoJAL-3621 update to intervalstore v1.1
gmungoc [Mon, 18 May 2020 14:57:13 +0000 (15:57 +0100)]
JAL-3621 update to intervalstore v1.1

4 years agoJAL-3529 test updated for revised signature of getDBRefs()
gmungoc [Mon, 18 May 2020 10:01:29 +0000 (11:01 +0100)]
JAL-3529 test updated for revised signature of getDBRefs()

4 years agoMerge branch 'Jalview-JS/develop' into develop
gmungoc [Mon, 18 May 2020 09:59:52 +0000 (10:59 +0100)]
Merge branch 'Jalview-JS/develop' into develop

Conflicts:
build.gradle
src/jalview/gui/PopupMenu.java
src/jalview/io/SequenceAnnotationReport.java
src/jalview/io/StockholmFile.java
src/jalview/util/DBRefUtils.java
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java

4 years agoJAL-3613 remove debug code committed in error
gmungoc [Mon, 18 May 2020 08:39:55 +0000 (09:39 +0100)]
JAL-3613 remove debug code committed in error

4 years agoJAL-3541 Fixed report path for build artifacts
Ben Soares [Fri, 15 May 2020 00:03:57 +0000 (01:03 +0100)]
JAL-3541 Fixed report path for build artifacts

4 years agoJAL-3541 Added mem setting and jvmArgs for cloverReporting
Ben Soares [Thu, 14 May 2020 20:11:47 +0000 (21:11 +0100)]
JAL-3541 Added mem setting and jvmArgs for cloverReporting

4 years agoJAL-3541 Individual tests now instrumented and reported. Added cloverConsoleReport.
Ben Soares [Thu, 14 May 2020 14:53:00 +0000 (15:53 +0100)]
JAL-3541 Individual tests now instrumented and reported.  Added cloverConsoleReport.

4 years agoJAL-3541 Helpers for running tests, and other commands headlessly
Ben Soares [Tue, 12 May 2020 22:05:58 +0000 (23:05 +0100)]
JAL-3541 Helpers for running tests, and other commands headlessly