Ben Soares [Fri, 4 Sep 2020 17:29:41 +0000 (18:29 +0100)]
JAL-3679 Added externally specified plugins dir to J2sPlugin check
Jim Procter [Thu, 10 Sep 2020 16:41:19 +0000 (17:41 +0100)]
JAL-3746 bump release version for 2.11.2 series (currently on develop)
gmungoc [Mon, 31 Aug 2020 15:46:54 +0000 (16:46 +0100)]
JAL-3518 removed unneeded override in ChimeraCommands
gmungoc [Thu, 18 Jun 2020 14:43:51 +0000 (15:43 +0100)]
JAL-3648 resize annotation panel after dragging to resize graph height
Ben Soares [Thu, 3 Sep 2020 15:27:44 +0000 (16:27 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
Jim Procter [Mon, 31 Aug 2020 17:05:59 +0000 (18:05 +0100)]
JAL-3680 merged description of individual cursor key actions
Jim Procter [Mon, 31 Aug 2020 16:49:18 +0000 (17:49 +0100)]
JAL-3732 - sequences can be moved up/down in cursor mode via alt-up/down arrow
JAL-3733 TODO - provide an undo for sequence/group up/down moves
gmungoc [Mon, 31 Aug 2020 15:10:57 +0000 (16:10 +0100)]
JAL-3018 Ensembl reviewed REST version updated to 13.0
gmungoc [Mon, 31 Aug 2020 15:00:22 +0000 (16:00 +0100)]
JAL-1191 use Cache.log for logging
gmungoc [Thu, 4 Jun 2020 16:22:29 +0000 (17:22 +0100)]
JAL-1191 reduce logging level for warnings
gmungoc [Mon, 24 Aug 2020 10:00:33 +0000 (11:00 +0100)]
JAL-3018 updated reviewed REST version to 12.0
Jim Procter [Mon, 17 Aug 2020 09:55:48 +0000 (10:55 +0100)]
Merge branch 'task/JAL-3597memoryLeakTest' into develop
Ben Soares [Thu, 13 Aug 2020 22:05:00 +0000 (23:05 +0100)]
JAL-3597 Increased heap passmark to <= 45MB and report smallest of failed attempts heap size
Ben Soares [Wed, 12 Aug 2020 11:00:57 +0000 (12:00 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
Jim Procter [Wed, 12 Aug 2020 10:15:54 +0000 (11:15 +0100)]
Merge branch 'task/JAL-3608_property_set_laf_and_tests' into develop
Ben Soares [Wed, 5 Aug 2020 21:57:13 +0000 (22:57 +0100)]
JAL-3691 Changed .toUppoerCase().startsWith(...) to .regionMatches(true,...) as upper-cased 'i' in Turkish is not 'I'.
Ben Soares [Tue, 4 Aug 2020 18:30:47 +0000 (19:30 +0100)]
JAL-3477 Improved command line arguments description in memory.html
Ben Soares [Tue, 4 Aug 2020 17:13:02 +0000 (18:13 +0100)]
JAL-3477 Added -help text for jvmmempc and jvmmemmax. Fixed typo and slight rewording in help/memory.html
Ben Soares [Mon, 3 Aug 2020 10:20:05 +0000 (11:20 +0100)]
JAL-3477 added help documentation for executable jar command line arguments -jvmmempc and -jvmmemmax
Jim Procter [Mon, 3 Aug 2020 09:40:46 +0000 (10:40 +0100)]
Merge branch 'bug/JAL-2983negativeSliderMin' into develop
Conflicts:
src/jalview/gui/FeatureSettings.java
src/jalview/gui/FeatureTypeSettings.java
Jim Procter [Wed, 29 Jul 2020 17:47:40 +0000 (18:47 +0100)]
JAL-3371 JAL-2983 don't modify 'extent' of slider - this is managed by look and feel
Jim Procter [Tue, 28 Jul 2020 12:36:00 +0000 (13:36 +0100)]
Merge branch 'feature/JAL-3615gzipXfam' into develop
Jim Procter [Tue, 28 Jul 2020 11:17:37 +0000 (12:17 +0100)]
JAL-3615 JAL-2656 missing import after cherrypick
Jim Procter [Tue, 28 Jul 2020 10:32:46 +0000 (11:32 +0100)]
JAL-2656 recognise non-HTTP URI input streams as gzipped by detecting the gzip magic header
Jim Procter [Tue, 28 Jul 2020 10:29:20 +0000 (11:29 +0100)]
JAL-2656 recognise Gzipped file input streams by their content, not their filename
Conflicts:
src/jalview/io/FileParse.java
cherypicked from 2.11.1.1 release patch
Jim Procter [Tue, 28 Jul 2020 10:18:56 +0000 (11:18 +0100)]
JAL-3615 update tests for Rfam/Pfam specific gzip endpoints
Jim Procter [Mon, 27 Jul 2020 14:10:11 +0000 (15:10 +0100)]
JAL-3697 show total number of features not shown
Jim Procter [Mon, 27 Jul 2020 14:05:30 +0000 (15:05 +0100)]
JAL-3696 log the error message from the exception to the console
Jim Procter [Mon, 27 Jul 2020 13:59:51 +0000 (14:59 +0100)]
JAL-3695 htsjdk 2.12 -> 2.23 (library change only, no code change. needs gradle refresh in eclipse)
gmungoc [Mon, 20 Jul 2020 08:17:29 +0000 (09:17 +0100)]
JAL-3597 slight tidying of code and Javadoc, passmark now heap <= 38MB
gmungoc [Tue, 14 Jul 2020 16:08:01 +0000 (17:08 +0100)]
JAL-1421 last change tidied up properly
gmungoc [Tue, 14 Jul 2020 08:44:46 +0000 (09:44 +0100)]
JAL-1421 types added to nameHash and nodeHash maps
gmungoc [Tue, 14 Jul 2020 08:43:50 +0000 (09:43 +0100)]
JAL-3597 additional references nulled, bug in test corrected
Ben Soares [Tue, 7 Jul 2020 23:47:55 +0000 (00:47 +0100)]
JAL-3608 Changes from code review CR-JAL-236
gmungoc [Tue, 7 Jul 2020 07:50:54 +0000 (08:50 +0100)]
JAL-1424 streamlined message checker, corrected applet lookup keys
gmungoc [Mon, 6 Jul 2020 14:59:53 +0000 (15:59 +0100)]
JAL-1424 slight tidying of reporting
gmungoc [Mon, 6 Jul 2020 14:57:57 +0000 (15:57 +0100)]
JAL-3311 JAL-3141 JAL-3144 tidying obsolete message bundle entries
gmungoc [Mon, 6 Jul 2020 11:57:24 +0000 (12:57 +0100)]
JAL-3518 Spanish text for 'write features'
gmungoc [Mon, 6 Jul 2020 11:37:41 +0000 (12:37 +0100)]
JAL-3570 JAL-3187 spanish translations for tabbed feature settings
gmungoc [Mon, 6 Jul 2020 09:05:25 +0000 (10:05 +0100)]
JAL-3570 updated external help links
gmungoc [Thu, 2 Jul 2020 16:24:28 +0000 (17:24 +0100)]
JAL-2656 JAL-3615 check response headers to test for gzipped url reply
gmungoc [Thu, 2 Jul 2020 14:28:36 +0000 (15:28 +0100)]
JAL-3615 used gzip endpoints for Pfam and Rfam
Jim Procter [Mon, 29 Jun 2020 16:50:24 +0000 (17:50 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Mon, 29 Jun 2020 16:46:57 +0000 (17:46 +0100)]
JAL-3675 2.11.1.1 release notes
Jim Procter [Mon, 29 Jun 2020 16:24:29 +0000 (17:24 +0100)]
JAL-3493 clear search highlights when escape/deselect all
Jim Procter [Mon, 29 Jun 2020 16:19:19 +0000 (17:19 +0100)]
JAL-3493 failing test - creates a highlight and column selection and then called the deselect all alignfjame action and checks if highlight and selection are still present.
Conflicts:
test/jalview/gui/SeqCanvasTest.java
gmungoc [Mon, 29 Jun 2020 15:53:51 +0000 (16:53 +0100)]
JAL-3674 more finessed asynchronous structure commands
gmungoc [Mon, 29 Jun 2020 10:55:14 +0000 (11:55 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Mon, 29 Jun 2020 10:04:05 +0000 (11:04 +0100)]
JAL-3518 corrected pulled up focusView() command
gmungoc [Mon, 29 Jun 2020 10:03:39 +0000 (11:03 +0100)]
JAL-3518 corrected action on pulled up closeViewer()
gmungoc [Sun, 28 Jun 2020 10:42:02 +0000 (11:42 +0100)]
JAL-3551 PyMOL command constants tidied
gmungoc [Sun, 28 Jun 2020 10:27:02 +0000 (11:27 +0100)]
JAL-3551 fit to window (zoom) command for PyMOL
Jim Procter [Fri, 26 Jun 2020 16:24:16 +0000 (17:24 +0100)]
JAL-3673 make sure font metrics are updated if dealing with reference sequence font !
Jim Procter [Fri, 26 Jun 2020 16:21:55 +0000 (17:21 +0100)]
JAL-3518 fix highlighting in Jalview for selections in ChimeraX
- needed to thread off the subsequent POST back to ChimeraX so ChimeraX can first hangup its GET to Jalview’s Rest API
Jim Procter [Fri, 26 Jun 2020 16:17:38 +0000 (17:17 +0100)]
JAL-3672 debug=false means no debug output
Jim Procter [Fri, 26 Jun 2020 16:17:22 +0000 (17:17 +0100)]
JAL-3672 more efficient when debug not enabled
Jim Procter [Fri, 26 Jun 2020 16:12:31 +0000 (17:12 +0100)]
JAL-3671 hardwire log4j.root logger to INFO to supress jetty and httpclient log output
gmungoc [Fri, 26 Jun 2020 09:39:08 +0000 (10:39 +0100)]
JAL-3518 tidy up asynchronous structure command execution
gmungoc [Thu, 25 Jun 2020 12:53:44 +0000 (13:53 +0100)]
JAL-2010 unused prototype method removed
gmungoc [Thu, 25 Jun 2020 11:50:47 +0000 (12:50 +0100)]
JAL-3518 pull up [get|list]ResidueAttributes to StructureCommandsI
gmungoc [Tue, 23 Jun 2020 15:55:42 +0000 (16:55 +0100)]
JAL-3518 separation of ChimeraXManager, pull up of closeViewer etc
gmungoc [Tue, 23 Jun 2020 11:10:42 +0000 (12:10 +0100)]
JAL-3518 pull up closeViewer() and external viewer process monitor
soares [Mon, 8 Jun 2020 13:36:41 +0000 (14:36 +0100)]
JAL-3446 new Jmol 15.1.3 jar added to j11lib, old j11lib Jmol-14.29.17-no_netscape.jar removed
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
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.
Ben Soares [Tue, 2 Jun 2020 22:03:57 +0000 (23:03 +0100)]
JAL-3225 Using Gradle Git-Version plugin to set gitHash and gitBranch
Using Gradle Git-Version instead of exec to run git directly allows
buildship to successfully import the project into eclipse without a
command line git installed. Essential for development within Eclipse in
Windows without having to install either gradle or git as command line
tools.
soares [Mon, 1 Jun 2020 14:54:16 +0000 (15:54 +0100)]
JAL-3225 small fixes for building within Eclipse
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
gmungoc [Mon, 1 Jun 2020 07:59:14 +0000 (08:59 +0100)]
JAL-3518 test result corrected
gmungoc [Mon, 1 Jun 2020 07:45:44 +0000 (08:45 +0100)]
JAL-3518 add alwaysRun = true [sigh]
gmungoc [Mon, 1 Jun 2020 07:30:08 +0000 (08:30 +0100)]
JAL-3518 more test coverage for structure commands
gmungoc [Fri, 29 May 2020 16:05:48 +0000 (17:05 +0100)]
JAL-2422 test updated
gmungoc [Fri, 29 May 2020 15:33:17 +0000 (16:33 +0100)]
Merge branch 'feature/JAL-3551Pymol' into develop
gmungoc [Fri, 29 May 2020 15:23:05 +0000 (16:23 +0100)]
JAL-3551 null pointer defence while structure files loading; comments
gmungoc [Thu, 28 May 2020 17:33:08 +0000 (18:33 +0100)]
JAL-3551 corrected Pymol open session command
gmungoc [Thu, 28 May 2020 17:27:31 +0000 (18:27 +0100)]
JAL-2422 correct ChimeraX save/open session commands; check for null
Ben Soares [Wed, 27 May 2020 16:37:12 +0000 (17:37 +0100)]
JAL-3541 ensure deletion of cloverReportDir
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
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
gmungoc [Tue, 26 May 2020 16:26:55 +0000 (17:26 +0100)]
JAL-1889 disable test failing on build server
soares [Tue, 26 May 2020 14:36:27 +0000 (15:36 +0100)]
Merge branch 'bug/JAL-3541_cloverReport_gradle_task_fails' into develop
soares [Tue, 26 May 2020 14:08:17 +0000 (15:08 +0100)]
JAL-3541 added a property/variable style comment to build.gradle
gmungoc [Tue, 26 May 2020 13:21:49 +0000 (14:21 +0100)]
JAL-3624 log when SIFTS mapping fails
gmungoc [Tue, 26 May 2020 12:38:55 +0000 (13:38 +0100)]
Merge branch 'feature/JAL-3624siftsInJS' into develop
gmungoc [Tue, 26 May 2020 11:51:17 +0000 (12:51 +0100)]
JAL-1761 pattern for structure viewer construction from project file
soares [Mon, 25 May 2020 23:14:15 +0000 (00:14 +0100)]
JAL-3541 selectively merged build.gradle and gradle.properties
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.
Jim Procter [Mon, 2 Mar 2020 10:42:07 +0000 (10:42 +0000)]
JAL-3407 redact Java 8 incompatible '<>' with anonymous inner classes
gmungoc [Thu, 21 May 2020 17:27:28 +0000 (18:27 +0100)]
JAL-3551 copy Jalview features to Pymol 'p' (with pull refactoring)
gmungoc [Thu, 21 May 2020 13:09:56 +0000 (14:09 +0100)]
JAL-2422 highlight ChimeraX selection (ChimeraX-1.0-rc-2020.05.21 +)
gmungoc [Wed, 20 May 2020 07:51:38 +0000 (08:51 +0100)]
JAL-3626 use Viewer.scriptWait() to send Jmol commands (Bob Hanson)
gmungoc [Tue, 19 May 2020 17:27:40 +0000 (18:27 +0100)]
JAL-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
gmungoc [Tue, 19 May 2020 16:27:32 +0000 (17:27 +0100)]
Merge branch 'develop' into feature/JAL-3551Pymol
Conflicts:
src/jalview/ext/jmol/JalviewJmolBinding.java
src/jalview/ext/jmol/JmolCommands.java
src/jalview/gui/AppJmol.java
src/jalview/gui/AppJmolBinding.java
src/jalview/gui/ChimeraViewFrame.java
src/jalview/gui/StructureViewerBase.java
src/jalview/jbgui/GPreferences.java
src/jalview/jbgui/GStructureViewer.java
src/jalview/project/Jalview2XML.java
gmungoc [Tue, 19 May 2020 10:50:41 +0000 (11:50 +0100)]
JAL-3624 use temp file for SIFT download in JS, correct unmarshalling
gmungoc [Mon, 18 May 2020 15:01:54 +0000 (16:01 +0100)]
JAL-3463 avoid Thread.sleep() as not supported in SwingJS
gmungoc [Mon, 18 May 2020 14:57:13 +0000 (15:57 +0100)]
JAL-3621 update to intervalstore v1.1
gmungoc [Mon, 18 May 2020 10:01:29 +0000 (11:01 +0100)]
JAL-3529 test updated for revised signature of getDBRefs()
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
gmungoc [Mon, 18 May 2020 08:39:55 +0000 (09:39 +0100)]
JAL-3613 remove debug code committed in error
git://source.jalview.org / jalview.git / log