Jim Procter [Wed, 2 Mar 2022 15:10:53 +0000 (15:10 +0000)]
JAL-3619 fix up error messages and try to bail quietly if the viewer doesn’t open
Jim Procter [Wed, 2 Mar 2022 14:49:56 +0000 (14:49 +0000)]
JAL-3619 fix up warning message and minimal patch to make sure failed-to-launch viewers tidy up after themselves.
Jim Procter [Wed, 2 Mar 2022 14:22:56 +0000 (14:22 +0000)]
JAL-3746 what’s new..
Jim Procter [Wed, 2 Mar 2022 13:05:39 +0000 (13:05 +0000)]
JAL-3746 release notes for JAL-3202 (JalviewJS)
Jim Procter [Wed, 2 Mar 2022 12:30:53 +0000 (12:30 +0000)]
JAL-3746 update release date and release notes/docs for JAL-1260, JAL-3821, JAL-3144, JAL-2226
Jim Procter [Mon, 28 Feb 2022 18:57:07 +0000 (18:57 +0000)]
JAL-3746 more what’s new and release notes
Jim Procter [Mon, 28 Feb 2022 18:30:02 +0000 (18:30 +0000)]
JAL-3503 2.11.2.0 release notes and docs
Jim Procter [Mon, 28 Feb 2022 17:57:49 +0000 (17:57 +0000)]
JAL-3746 JAL-3551 update pymol docs and what’s new text
Jim Procter [Mon, 28 Feb 2022 11:59:28 +0000 (11:59 +0000)]
JAL-3746 document -no-annotation cli arg
Jalview Development Admin [Wed, 23 Feb 2022 18:55:37 +0000 (18:55 +0000)]
Merge branch 'improvement/JAL-3830_install4j9_macos_setup_application' of source.jalview.org/git/jalview into improvement/JAL-3830_install4j9_macos_setup_application
Jalview Development Admin [Wed, 23 Feb 2022 18:54:57 +0000 (18:54 +0000)]
JAL-3830 temporarily disable the setup screen for OSX dmgs until we can properly document its use
Jalview Development Admin [Wed, 23 Feb 2022 17:23:42 +0000 (17:23 +0000)]
JAL-3796 additional steps for notarization
Jim Procter [Thu, 17 Feb 2022 17:28:24 +0000 (17:28 +0000)]
Merge branch 'develop' into improvement/JAL-3830_install4j9_macos_setup_application
Jim Procter [Thu, 17 Feb 2022 17:15:38 +0000 (17:15 +0000)]
JAL-3551 patch superpose test for additional undo dis/enable commands
Jim Procter [Thu, 17 Feb 2022 17:10:50 +0000 (17:10 +0000)]
JAL-3823 JAL-3830 update gradle plugin for install4j to 9.0.6
Jim Procter [Thu, 17 Feb 2022 17:04:14 +0000 (17:04 +0000)]
Merge branch 'develop' into improvement/JAL-3830_install4j9_macos_setup_application
Jim Procter [Thu, 17 Feb 2022 15:05:21 +0000 (15:05 +0000)]
JAL-3959 add key retrieval urls that support CORS needed by JalviewJS
Jim Procter [Thu, 17 Feb 2022 12:58:37 +0000 (12:58 +0000)]
JAL-3746 more release notes and docs: JAL-3863 JAL-3745
Jim Procter [Wed, 16 Feb 2022 18:43:48 +0000 (18:43 +0000)]
JAL-3746 release notes.. in progress
Jim Procter [Wed, 16 Feb 2022 18:43:23 +0000 (18:43 +0000)]
JAL-3551 - wrap pair_fit with undo_disable and undo_enable
Jim Procter [Wed, 16 Feb 2022 16:34:56 +0000 (16:34 +0000)]
JAL-3837 GPL license on splashscreen (finally !) and added link to discourse.jalview.org to replace mailing list
Jim Procter [Wed, 16 Feb 2022 15:51:23 +0000 (15:51 +0000)]
JAL-3949 report Pymol XMLRPC port via log.info
Jim Procter [Tue, 15 Feb 2022 17:35:16 +0000 (17:35 +0000)]
JAL-1761 backbone type parameter for configuring which atoms are used for superposition of structures
Jim Procter [Tue, 15 Feb 2022 16:55:17 +0000 (16:55 +0000)]
JAL-1761 need to pass molecule type when generating superposition commands
Jim Procter [Tue, 15 Feb 2022 16:54:26 +0000 (16:54 +0000)]
JAL-3551 patch test for altloc handling atom spec in superposition code
Jim Procter [Tue, 15 Feb 2022 16:47:32 +0000 (16:47 +0000)]
JAL-1761 need to pass molecule type when generating superposition commands
Jim Procter [Tue, 15 Feb 2022 16:46:02 +0000 (16:46 +0000)]
JAL-3906 use indicate to highlight current mousedOver residue in Jalview in a Pymol view
Jim Procter [Tue, 15 Feb 2022 16:45:11 +0000 (16:45 +0000)]
JAL-3746 update release date to later in Feb 2022
Jim Procter [Tue, 15 Feb 2022 16:44:40 +0000 (16:44 +0000)]
JAL-3551 pymol documentation
Jim Procter [Mon, 14 Feb 2022 23:02:41 +0000 (23:02 +0000)]
Merge branch 'task/r_2_11_2/JAL-3956_alphaFill_authoritative_IDs' into develop
Jim Procter [Mon, 14 Feb 2022 22:58:01 +0000 (22:58 +0000)]
JAL-3551
Jim Procter [Mon, 14 Feb 2022 14:03:39 +0000 (14:03 +0000)]
JAL-3956 - PDBEntry objects constructed from 3D-Beacons have authoritative IDs overriding any embedded IDs
Jim Procter [Sat, 12 Feb 2022 11:49:56 +0000 (11:49 +0000)]
Merge branch 'update/JAL-3949_jalview_bin_Console_to_cure_sanity_even_more' into develop
Conflicts:
test/jalview/bin/CommandLineOperations.java
Ben Soares [Sat, 12 Feb 2022 10:09:07 +0000 (10:09 +0000)]
JAL-3949 fix testProps path and make line count more accurate
Jim Procter [Fri, 11 Feb 2022 18:52:17 +0000 (18:52 +0000)]
JAL-3949 increase command line ops test timeout
Jim Procter [Fri, 11 Feb 2022 18:44:19 +0000 (18:44 +0000)]
JAL-3949 ensure Jalview command line ops setup actually quits after SETUP_TIME milliseconds - seems there’s less stderr noise than before !
Jim Procter [Fri, 11 Feb 2022 17:27:42 +0000 (17:27 +0000)]
Merge branch 'update/JAL-3949_jalview_bin_Console_to_cure_sanity_even_more' into develop
Jim Procter [Fri, 11 Feb 2022 17:09:04 +0000 (17:09 +0000)]
JAL-3931 fix - escape % symbols after urlencoding
Ben Soares [Fri, 11 Feb 2022 15:43:34 +0000 (15:43 +0000)]
Merge branch 'update/JAL-3949_jalview_bin_Console_to_cure_sanity_even_more' of https://source.jalview.org/git/jalview into update/JAL-3949_jalview_bin_Console_to_cure_sanity_even_more
Ben Soares [Fri, 11 Feb 2022 15:43:30 +0000 (15:43 +0000)]
JLogger loglevel check on whether to call the actual logger or not. New factory methods with Class.
Jim Procter [Fri, 11 Feb 2022 15:27:51 +0000 (15:27 +0000)]
JAL-3949 - refactor logging from jalview.bin.Cache to jalview.bin.Console
Conflicts:
src/jalview/bin/Jalview.java
Ben Soares [Fri, 11 Feb 2022 14:15:09 +0000 (14:15 +0000)]
JAL-3949 fixed failing commandlinetests due to more output and line count limit
Ben Soares [Fri, 11 Feb 2022 14:14:39 +0000 (14:14 +0000)]
JAL-3949 added Java Console autoscrolling help paragraph
Ben Soares [Fri, 11 Feb 2022 12:39:51 +0000 (12:39 +0000)]
JAL-3949 read ~/.jalview_properties before initialising the logging
Ben Soares [Fri, 11 Feb 2022 03:35:57 +0000 (03:35 +0000)]
Merge branch 'develop' into update/JAL-3949_abstracted_logging_for_jalviewjs_and_sanity
Ben Soares [Fri, 11 Feb 2022 03:34:22 +0000 (03:34 +0000)]
JAL-3949 Complete new abstracted logging framework in jalview.log. Updated log calls for this. Removal of jalview.javascript.log4j. Improvements to the Java Console (controllable autoscrolling).
Jim Procter [Thu, 10 Feb 2022 15:45:23 +0000 (15:45 +0000)]
Merge branch 'bug/JAL-3523_cwd_not_preserved' into develop
rebuilt getdown jars - did not bump version
Jim Procter [Mon, 7 Feb 2022 16:07:33 +0000 (16:07 +0000)]
JAL-3186 remove ‘Variable Colour’ from the sequence feature settings popup menu
Ben Soares [Fri, 4 Feb 2022 18:08:09 +0000 (18:08 +0000)]
JAL-3949 An attempt at converting to Log4j 2 -- no output achieved!
Jim Procter [Fri, 4 Feb 2022 14:34:20 +0000 (14:34 +0000)]
Merge branch 'bug/JAL-3806_mappingCoversSequence_for2112' into develop
Combines patches for JAL-3806 prior to redaction of shared CDS dataset sequences with patches for JAL-3673
Conflicts:
src/jalview/datamodel/AlignedCodonFrame.java
src/jalview/util/MappingUtils.java
test/jalview/util/MappingUtilsTest.java
Jim Procter [Fri, 4 Feb 2022 13:19:48 +0000 (13:19 +0000)]
JAL-3806 JAL-3725 update tests since CDS mappings now exclude the stop codon
Jim Procter [Fri, 4 Feb 2022 13:13:02 +0000 (13:13 +0000)]
JAL-3806 require mapping extent covers both sequence’s dataset sequence to avoid spurious mappings from overlapping CDS
Ben Soares [Thu, 3 Feb 2022 19:38:32 +0000 (19:38 +0000)]
JAL-3949 upgraded log4j to 2.17.1 (no actual known vulnerabilities\!), though this doesn't fix the issue
Jim Procter [Thu, 3 Feb 2022 14:59:31 +0000 (14:59 +0000)]
JAL-3806 use the covers() test for each selected sequence and the complementary alignment’s sequence as a filter for direct CDS-Protein mappings (ensures overlapping CDS coding for distinct proteins do not all get selected)
Jim Procter [Thu, 3 Feb 2022 14:20:11 +0000 (14:20 +0000)]
JAL-3806 use same logic as for mouse over highlighting to work out extent of selected region in complement alignment
Jim Procter [Thu, 3 Feb 2022 13:41:25 +0000 (13:41 +0000)]
JAL-3806 todo - problem seems to be Protein:Many CDS are not selected
Jim Procter [Thu, 3 Feb 2022 13:18:44 +0000 (13:18 +0000)]
JAL-2305 comments re testFindXrefSequences_withFetch is failing - looks like test data needs to be revised for assumptions made by CrossRef about sequences retrieved from dbsources
Ben Soares [Sat, 29 Jan 2022 01:00:00 +0000 (01:00 +0000)]
JAL-3830 JAL-3420 added new jvl_file to install4j9 template
Ben Soares [Sat, 29 Jan 2022 00:57:07 +0000 (00:57 +0000)]
Merge branch 'develop' into improvement/JAL-3830_install4j9_macos_setup_application
Ben Soares [Fri, 28 Jan 2022 18:22:54 +0000 (18:22 +0000)]
Merge branch 'develop' into improvement/JAL-3420_match_jvl_icon_with_new_website_jvl_icon
Ben Soares [Fri, 28 Jan 2022 18:22:27 +0000 (18:22 +0000)]
new jvl_file svg, png, ico and icns files, and changed references to Jalview-Launch to jvl_file
Jim Procter [Fri, 28 Jan 2022 17:24:15 +0000 (17:24 +0000)]
JAL-3137 tests are for linux only
Jim Procter [Fri, 28 Jan 2022 17:08:35 +0000 (17:08 +0000)]
Merge branch 'merge/develop_JAL-3725' into develop
Conflicts:
src/jalview/gui/PopupMenu.java
Jim Procter [Thu, 27 Jan 2022 14:21:39 +0000 (14:21 +0000)]
Merge branch 'bug/JAL-3633_read_proxy_settings_from_jalview_properties_in_getdown' into develop
Conflicts:
src/jalview/bin/MemorySetting.java
Jim Procter [Wed, 26 Jan 2022 23:41:08 +0000 (23:41 +0000)]
JAL-3763 (for whatever reason) need to increase timeout for command line ops to 10.5s (OSX Monterey, MBP late 2018)
Jim Procter [Wed, 26 Jan 2022 23:32:26 +0000 (23:32 +0000)]
JAL-3746 note about adding JAL-3700,JAL-3751,JAL-3763 release notes
Jim Procter [Wed, 26 Jan 2022 23:26:04 +0000 (23:26 +0000)]
Merge branch 'merge/develop_task/JAL-3763_newDatasetForCds' into develop
Jim Procter [Wed, 26 Jan 2022 19:54:17 +0000 (19:54 +0000)]
JAL-3763 (for whatever reason) need to increase timeout for command line ops to 10.5s (OSX Monterey, MBP late 2018)
Jim Procter [Wed, 26 Jan 2022 19:36:23 +0000 (19:36 +0000)]
Merge branch 'task/JAL-3763_newDatasetForCds' into merge/develop_task/JAL-3763_newDatasetForCds
Conflicts:
src/jalview/analysis/AlignmentUtils.java
src/jalview/util/MapList.java
test/jalview/util/MapListTest.java
test/jalview/util/MappingUtilsTest.java
gmungoc [Thu, 28 Jan 2021 16:56:55 +0000 (16:56 +0000)]
JAL-3806 (2.11.2 version) more lax allowance (3 positions) for stop codon
Jim Procter [Thu, 6 Jan 2022 12:29:01 +0000 (12:29 +0000)]
JAL-3806 JAL-3725 propagate relaxed criteria for stop codon truncation from EMBLXmlSource to EMBLFlatFile parser
gmungoc [Thu, 27 Aug 2020 15:02:06 +0000 (16:02 +0100)]
JAL-3725 restrict mapped virtual feature location to mapped region
gmungoc [Thu, 27 Aug 2020 14:44:45 +0000 (15:44 +0100)]
JAL-3725 helper methods for computing mapped feature range overlap
gmungoc [Thu, 27 Aug 2020 14:40:22 +0000 (15:40 +0100)]
JAL-3725 exclude stop codon from CDS-to-protein mapping
Jim Procter [Tue, 18 Jan 2022 12:24:23 +0000 (12:24 +0000)]
JAL-3940 update 2.11.2 release notes for 2.11.1.7 patch release (again)
Jim Procter [Mon, 17 Jan 2022 12:36:40 +0000 (12:36 +0000)]
JAL-3940 update 2.11.2 release notes for 2.11.1.7 patch release
Jim Procter [Mon, 17 Jan 2022 11:54:32 +0000 (11:54 +0000)]
JAL-3746 possible release date 1st Feb 2022
Jim Procter [Mon, 17 Jan 2022 11:54:16 +0000 (11:54 +0000)]
JAL-3746 Release notes for patch JAL-3702 JAL-3915
Jim Procter [Mon, 17 Jan 2022 11:45:47 +0000 (11:45 +0000)]
Merge branch 'bug/JAL-3703_saving_a_file_in_Windows_10_fails' into develop
Ben Soares [Wed, 12 Jan 2022 12:32:06 +0000 (12:32 +0000)]
JAL-3703 Test that fails in Windows only, and only when the file handle isn't relinquished
Ben Soares [Tue, 11 Jan 2022 20:13:57 +0000 (20:13 +0000)]
JAL-3703 fix Gff3 shared InputStream with embedded FASTA data
Ben Soares [Tue, 11 Jan 2022 16:04:49 +0000 (16:04 +0000)]
close filehandles straight after parse, without setting an error
Ben Soares [Mon, 10 Jan 2022 20:31:29 +0000 (20:31 +0000)]
JAL-3937 enable AIA download of intermediate certificates when needed
Jim Procter [Thu, 6 Jan 2022 09:58:49 +0000 (09:58 +0000)]
JAL-3746 update release history for 2.11.1.5 and 2.11.1.6 patch releases
Jim Procter [Thu, 6 Jan 2022 09:47:28 +0000 (09:47 +0000)]
Merge branch 'critical/JAL-3933_log4j_update_for_develop_branch' into develop
Ben Soares [Wed, 22 Dec 2021 11:17:41 +0000 (11:17 +0000)]
Merge branch 'develop' into critical/JAL-3933_log4j_update_for_develop_branch
Ben Soares [Wed, 22 Dec 2021 11:12:37 +0000 (11:12 +0000)]
JAL-3934 updated log4j from 2.16.0 to 2.17.0
Ben Soares [Wed, 15 Dec 2021 13:23:16 +0000 (13:23 +0000)]
JAL-3933 updated THIRDPARTYLIBS
Ben Soares [Wed, 15 Dec 2021 13:16:11 +0000 (13:16 +0000)]
JAL-3933 updated THIRDPARTYLIBS
Jim Procter [Wed, 15 Dec 2021 10:38:22 +0000 (10:38 +0000)]
JAL-3933 remove obsolete Castor logging configuration
Jim Procter [Wed, 15 Dec 2021 10:36:18 +0000 (10:36 +0000)]
JAL-3933 configure root logger console appender to stderr (2.11.2 version)
Ben Soares [Tue, 14 Dec 2021 23:23:08 +0000 (23:23 +0000)]
JAL-3933 updated log4j and slf4j jars with log4j1.2 compatibility API jar. Removed log4j from jabaws-min-client and Jmol jars
Jim Procter [Mon, 13 Dec 2021 18:17:33 +0000 (18:17 +0000)]
JAL-3829 isCanonical should by default be false - ensure JalviewJS offers 3d-beacons search for example project
Jim Procter [Mon, 13 Dec 2021 17:49:19 +0000 (17:49 +0000)]
JAL-3855 JAL-3829 don’t need to make up alphafold model retrieval URL when we’ve been given it
Jim Procter [Mon, 13 Dec 2021 14:15:06 +0000 (14:15 +0000)]
JAL-3929 preserve lowercase pdbid in group name for transferred features
Jim Procter [Wed, 8 Dec 2021 18:58:42 +0000 (18:58 +0000)]
Merge branch 'to_merge/r2_11_2/JAL-3904_improved_alignpanelAPI_autoshowview' into develop
Jim Procter [Wed, 8 Dec 2021 18:53:57 +0000 (18:53 +0000)]
JAL-3551 pymol docs - work in progress
Jim Procter [Wed, 8 Dec 2021 18:52:45 +0000 (18:52 +0000)]
JAL-3929 don’t use the url encoded pdbId in feature group when transferring features from associated structure to a sequence
Jim Procter [Wed, 8 Dec 2021 15:59:38 +0000 (15:59 +0000)]
JAL-3616 update messages/tooltips/menu items to use getViewerName() for chimera/x/pymol
Jim Procter [Wed, 8 Dec 2021 15:48:37 +0000 (15:48 +0000)]
JAL-3551 JAL-3931 view pymol commands/responses in Log.trace
git://source.jalview.org / jalview.git / log