jalview.git
2 years agoJAL-3675 release notes for JAL-3750 JAL-3751 Release_2_11_1_1
Jim Procter [Thu, 17 Sep 2020 12:38:15 +0000 (13:38 +0100)]
JAL-3675 release notes for JAL-3750 JAL-3751

2 years agoMerge branch 'patch/JAL-3750_JAL-3741_https_patch' into releases/Release_2_11_1_Branch
Jim Procter [Thu, 17 Sep 2020 11:28:03 +0000 (12:28 +0100)]
Merge branch 'patch/JAL-3750_JAL-3741_https_patch' into releases/Release_2_11_1_Branch

2 years agoJAL-3741 http to https (and jar to jvp for exampleFile defaults!)
Jim Procter [Thu, 17 Sep 2020 11:19:40 +0000 (12:19 +0100)]
JAL-3741 http to https (and jar to jvp for exampleFile defaults!)

2 years agoJAL-3750 parse protocol before checking if argument to -open can be opened as a file
Jim Procter [Thu, 17 Sep 2020 11:09:42 +0000 (12:09 +0100)]
JAL-3750 parse protocol before checking if argument to -open can be opened as a file

2 years agoJAL-3675 patch release date 17th September 2020
Jim Procter [Thu, 17 Sep 2020 10:35:46 +0000 (11:35 +0100)]
JAL-3675 patch release date 17th September 2020

2 years agoJAL-3675 logged JAL-3748 as known defect
Jim Procter [Tue, 15 Sep 2020 17:05:24 +0000 (18:05 +0100)]
JAL-3675 logged JAL-3748 as known defect

2 years agoJAL-3765 JAL-3718 release notes
Jim Procter [Tue, 15 Sep 2020 15:48:48 +0000 (16:48 +0100)]
JAL-3765 JAL-3718 release notes

2 years agoMerge branch 'patch/JAL-3718_fixed_getdown_patched_for_Release_2_11_1_Branch' into...
Jim Procter [Tue, 15 Sep 2020 15:34:53 +0000 (16:34 +0100)]
Merge branch 'patch/JAL-3718_fixed_getdown_patched_for_Release_2_11_1_Branch' into releases/Release_2_11_1_Branch

2 years agoJAL-3718 Fixed getdown auto-update. This commit Getdown jars and version files.
Ben Soares [Tue, 15 Sep 2020 15:17:18 +0000 (16:17 +0100)]
JAL-3718 Fixed getdown auto-update. This commit Getdown jars and version files.

2 years agoJAL-3718 force re-initialise of getdown.txt file when new getdown.txt downloaded...
Ben Soares [Mon, 14 Sep 2020 22:23:11 +0000 (23:23 +0100)]
JAL-3718 force re-initialise of getdown.txt file when new getdown.txt downloaded from appbase. getdown src files

2 years agoJAL-3675 typo in release notes :(
Jim Procter [Tue, 15 Sep 2020 12:52:02 +0000 (13:52 +0100)]
JAL-3675 typo in release notes :(

2 years agoJAL-3675 update release date and release notes for JAL-3732
Jim Procter [Tue, 15 Sep 2020 11:43:35 +0000 (12:43 +0100)]
JAL-3675 update release date and release notes for JAL-3732

2 years agoJAL-3648 resize annotation panel after dragging to resize graph height
gmungoc [Thu, 18 Jun 2020 14:43:51 +0000 (15:43 +0100)]
JAL-3648 resize annotation panel after dragging to resize graph height

2 years agoJAL-3675 update release date and release notes for JAL-3280
Jim Procter [Thu, 3 Sep 2020 12:43:40 +0000 (13:43 +0100)]
JAL-3675 update release date and release notes for JAL-3280

2 years agoMerge branch 'improvement/JAL-3280_Migrate_the_VersionChecker_service_to_build_proper...
Jim Procter [Thu, 3 Sep 2020 11:20:22 +0000 (12:20 +0100)]
Merge branch 'improvement/JAL-3280_Migrate_the_VersionChecker_service_to_build_properties' into releases/Release_2_11_1_Branch

2 years agoJAL-3675 whats new, logging and release notes tidying for 2.11.1.1.
Jim Procter [Thu, 3 Sep 2020 10:42:43 +0000 (11:42 +0100)]
JAL-3675 whats new, logging and release notes tidying for 2.11.1.1.

2 years agoJAL-3676 rework logging docs.
Jim Procter [Thu, 3 Sep 2020 09:52:04 +0000 (10:52 +0100)]
JAL-3676 rework logging docs.

2 years agoMerge branch 'bug/JAL-3718_Getdown_does_not_autoupdate_correctly' into releases/Relea...
Jim Procter [Thu, 3 Sep 2020 08:07:42 +0000 (09:07 +0100)]
Merge branch 'bug/JAL-3718_Getdown_does_not_autoupdate_correctly' into releases/Release_2_11_1_Branch

2 years agoJAL-3676 remove mention of Castor
Jim Procter [Thu, 3 Sep 2020 07:07:48 +0000 (08:07 +0100)]
JAL-3676 remove mention of Castor

2 years agoJAL-3675 tweak release notes for JAL-3667, JAL-3702
Jim Procter [Thu, 3 Sep 2020 06:41:45 +0000 (07:41 +0100)]
JAL-3675 tweak release notes for JAL-3667, JAL-3702

2 years agoJAL-3675 update sequence fetcher service documentation for JAL-3692 (ENA Flatfile...
Jim Procter [Thu, 3 Sep 2020 06:21:56 +0000 (07:21 +0100)]
JAL-3675 update sequence fetcher service documentation for JAL-3692 (ENA Flatfile) and refreshed links for other endpoints.

2 years agoJAL-3280 Test for remote release build_properties file version check improvement/JAL-3280_Migrate_the_VersionChecker_service_to_build_properties
Ben Soares [Wed, 2 Sep 2020 17:25:40 +0000 (18:25 +0100)]
JAL-3280 Test for remote release build_properties file version check

2 years agoJAL-3280 fixes after CR-JAL-241. Now only checking release build_properties.
Ben Soares [Tue, 1 Sep 2020 16:45:21 +0000 (17:45 +0100)]
JAL-3280 fixes after CR-JAL-241. Now only checking release build_properties.

2 years agoJAL-3280 Pass appbase and appdir from getdown to jalvew. Check appbase (defaults...
Ben Soares [Mon, 31 Aug 2020 17:38:15 +0000 (18:38 +0100)]
JAL-3280 Pass appbase and appdir from getdown to jalvew. Check appbase (defaults to release appbase) for build_properties VERSION insteadl of jnlp file.

2 years agoJAL-3680 merged description of individual cursor key actions
Jim Procter [Mon, 31 Aug 2020 17:05:59 +0000 (18:05 +0100)]
JAL-3680 merged description of individual cursor key actions

2 years agoJAL-3732 - sequences can be moved up/down in cursor mode via alt-up/down arrow
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

2 years agoJAL-3676 adding Axis and Castor loggging properties to the help text
Ben Soares [Fri, 28 Aug 2020 10:10:33 +0000 (11:10 +0100)]
JAL-3676 adding Axis and Castor loggging properties to the help text

2 years agoJAL-3676 Documentation in Help for Java Console, Logging and Reporting Bugs
Ben Soares [Thu, 27 Aug 2020 14:53:02 +0000 (15:53 +0100)]
JAL-3676 Documentation in Help for Java Console, Logging and Reporting Bugs

2 years agoMerge branch 'releases/Release_2_11_1_Branch' into merge/JAL_1842+JAL-3509+releases_R... merge/JAL_1842+JAL-3509+releases_Release_2_11_1_Branch
Ben Soares [Thu, 27 Aug 2020 09:09:13 +0000 (10:09 +0100)]
Merge branch 'releases/Release_2_11_1_Branch' into merge/JAL_1842+JAL-3509+releases_Release_2_11_1_Branch

2 years agoreport JAL-3127 as known defect (fix targeted for 2.11.2)
Jim Procter [Tue, 25 Aug 2020 16:45:53 +0000 (17:45 +0100)]
report JAL-3127 as known defect (fix targeted for 2.11.2)

2 years agoJAL-3671 hardwire log4j.root logger to INFO to supress jetty and httpclient log output
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

2 years agoJAL-3675 2.11.1.1 java 8 compatible patch for JAL-3615 from feature/JAL-3615gzipXfam
Jim Procter [Fri, 21 Aug 2020 10:45:26 +0000 (11:45 +0100)]
JAL-3675 2.11.1.1 java 8 compatible patch for JAL-3615 from feature/JAL-3615gzipXfam

2 years agoJAL-3718 Added digestonly key to getdown.txt to copy file to alt or release when...
Ben Soares [Tue, 18 Aug 2020 23:38:12 +0000 (00:38 +0100)]
JAL-3718 Added digestonly key to getdown.txt to copy file to alt or release when building, and to be included in the getdown digest.  This key is completely ignored by the getdown-launcher.  Looks in j8/j11digestonly.

2 years agoJAL-3692 parse multiline CDS location correctly
gmungoc [Tue, 18 Aug 2020 13:59:12 +0000 (14:59 +0100)]
JAL-3692 parse multiline CDS location correctly

2 years agoJAL-3676 Start of documentation in help pages logging.html
Ben Soares [Tue, 18 Aug 2020 07:40:33 +0000 (08:40 +0100)]
JAL-3676 Start of documentation in help pages logging.html

2 years agoJAL-3675 release notes for JAL-3691
Jim Procter [Mon, 17 Aug 2020 15:56:52 +0000 (16:56 +0100)]
JAL-3675 release notes for JAL-3691

2 years agoMerge branch 'patch/JAL-3691_No_score_models_available' into releases/Release_2_11_1_...
Jim Procter [Mon, 17 Aug 2020 15:53:31 +0000 (16:53 +0100)]
Merge branch 'patch/JAL-3691_No_score_models_available' into releases/Release_2_11_1_Branch

2 years agoJAL-3675 JAL-3561 documented in release notes
Jim Procter [Mon, 17 Aug 2020 15:49:16 +0000 (16:49 +0100)]
JAL-3675 JAL-3561 documented in release notes

2 years agoJAL-3675 report JAL-3702 as known defect
Jim Procter [Mon, 17 Aug 2020 15:38:49 +0000 (16:38 +0100)]
JAL-3675 report JAL-3702 as known defect

2 years agoMerge branch 'patch/JAL-3561_JAL-3660_fileformatexport_CLI' into releases/Release_2_1...
Jim Procter [Mon, 17 Aug 2020 15:25:07 +0000 (16:25 +0100)]
Merge branch 'patch/JAL-3561_JAL-3660_fileformatexport_CLI' into releases/Release_2_11_1_Branch

2 years agoJAL-3712 fix typos for rebuilding/updating getdown jars and added mention of mvn_cmd...
Jim Procter [Mon, 17 Aug 2020 15:09:26 +0000 (16:09 +0100)]
JAL-3712 fix typos for rebuilding/updating getdown jars and added mention of mvn_cmd in the getdown building help.

2 years agoJAL-3490 JAL-3675 release notes, update Find dialog image in help and tidy up documen...
Jim Procter [Mon, 17 Aug 2020 11:13:03 +0000 (12:13 +0100)]
JAL-3490 JAL-3675 release notes, update Find dialog image in help and tidy up documentation for 2.11.1.1

2 years agoMerge branch 'patch/Release_2_11_1_Branch_patch_JAL-3490' into releases/Release_2_11_...
Jim Procter [Mon, 17 Aug 2020 10:03:57 +0000 (11:03 +0100)]
Merge branch 'patch/Release_2_11_1_Branch_patch_JAL-3490' into releases/Release_2_11_1_Branch

2 years agoJAL-3675 JAL-3597 release notes
Jim Procter [Mon, 17 Aug 2020 09:51:05 +0000 (10:51 +0100)]
JAL-3675 JAL-3597 release notes

2 years agoMerge branch 'patch/JAL-3597_for_Release_2_11_1_Branch' into releases/Release_2_11_1_...
Jim Procter [Mon, 17 Aug 2020 09:03:47 +0000 (10:03 +0100)]
Merge branch 'patch/JAL-3597_for_Release_2_11_1_Branch' into releases/Release_2_11_1_Branch

2 years agoJAL-3676 More explicit tooltip about resetting log level on Console close. Also clari...
Ben Soares [Fri, 14 Aug 2020 12:01:06 +0000 (13:01 +0100)]
JAL-3676 More explicit tooltip about resetting log level on Console close. Also clarified code to set initial log level and re-set on close to previously set level.

2 years agoJAL-3597 Increased heap passmark to <= 45MB and report smallest of failed attempts...
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

2 years agoJAL-3597 slight tidying of code and Javadoc, passmark now heap <= 38MB
gmungoc [Mon, 20 Jul 2020 08:17:29 +0000 (09:17 +0100)]
JAL-3597 slight tidying of code and Javadoc, passmark now heap <= 38MB

2 years agoJAL-3597 additional references nulled, bug in test corrected
gmungoc [Tue, 14 Jul 2020 08:43:50 +0000 (09:43 +0100)]
JAL-3597 additional references nulled, bug in test corrected

2 years agoJAL-3675 brought forward patch to build.gradle for changed main class variable in...
Jim Procter [Thu, 13 Aug 2020 16:51:44 +0000 (17:51 +0100)]
JAL-3675 brought forward patch to build.gradle for changed main class variable in build.properties

2 years agoMerge branch 'releases/Release_2_11_1_Branch' of http://source.jalview.org/git/jalvie...
Jim Procter [Thu, 13 Aug 2020 14:53:53 +0000 (15:53 +0100)]
Merge branch 'releases/Release_2_11_1_Branch' of source.jalview.org/git/jalview into releases/Release_2_11_1_Branch

2 years agoJAL-3676 Removed BACKUPFILESPRESETENTRY logging for opening the file browser. Changed...
Ben Soares [Wed, 12 Aug 2020 12:48:57 +0000 (13:48 +0100)]
JAL-3676 Removed BACKUPFILESPRESETENTRY logging for opening the file browser. Changed most BACKUPFILES logging from DEBUG to TRACE level. Minor wording changes.

2 years agoJAL-3675 added JAL-3576 as known defect (colocated features appear in different order...
Jim Procter [Wed, 12 Aug 2020 12:29:23 +0000 (13:29 +0100)]
JAL-3675 added JAL-3576 as known defect (colocated features appear in different order when exported/reimported)

2 years agoJAL-3608 Changes from code review CR-JAL-236
Ben Soares [Tue, 7 Jul 2020 23:47:55 +0000 (00:47 +0100)]
JAL-3608 Changes from code review  CR-JAL-236

 Conflicts:
src/jalview/bin/Jalview.java

2 years agoJAL-3675 fix issue attribution for JAL-3667 release note line
Jim Procter [Tue, 11 Aug 2020 15:24:26 +0000 (16:24 +0100)]
JAL-3675 fix issue attribution for JAL-3667 release note line

2 years agoJAL-3675 update release notes for JAL-3673 and tested merge of additional patch for...
Jim Procter [Tue, 11 Aug 2020 14:54:24 +0000 (15:54 +0100)]
JAL-3675 update release notes for JAL-3673 and tested merge of additional patch for JAL-2983

2 years agoJAL-3673 make sure font metrics are updated if dealing with reference sequence font !
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 !

2 years agoMerge branch 'bug/JAL-2983negativeSliderMin' into releases/Release_2_11_1_Branch
Jim Procter [Tue, 11 Aug 2020 14:01:10 +0000 (15:01 +0100)]
Merge branch 'bug/JAL-2983negativeSliderMin' into releases/Release_2_11_1_Branch

2 years agoJAL-3371 more fine-grained slider; set Param slider to initial default bug/JAL-2983negativeSliderMin
gmungoc [Tue, 11 Aug 2020 09:35:32 +0000 (10:35 +0100)]
JAL-3371 more fine-grained slider; set Param slider to initial default

2 years agoJAL-3490 match count independent of contiguous matches count patch/Release_2_11_1_Branch_patch_JAL-3490
gmungoc [Thu, 6 Aug 2020 08:49:23 +0000 (09:49 +0100)]
JAL-3490 match count independent of contiguous matches count

2 years agoJAL-3691 toUpperCase(Locale.ROOT) for all standard file format operations
Jim Procter [Mon, 10 Aug 2020 14:10:35 +0000 (15:10 +0100)]
JAL-3691 toUpperCase(Locale.ROOT) for all standard file format operations

2 years agoMerge branch 'releases/Release_2_11_1_Branch' into patch/JAL-3691_No_score_models_ava...
Jim Procter [Mon, 10 Aug 2020 14:02:53 +0000 (15:02 +0100)]
Merge branch 'releases/Release_2_11_1_Branch' into patch/JAL-3691_No_score_models_available

2 years agoJAL-3628 JAL-3708 call Cache.initLogger() before using Cache.log in static methods...
Jim Procter [Mon, 10 Aug 2020 14:01:23 +0000 (15:01 +0100)]
JAL-3628 JAL-3708 call Cache.initLogger() before using Cache.log in static methods with no class-level guarantee logs are initialised

2 years agoJAL-3691 Changed .toUppoerCase().startsWith(...) to .regionMatches(true,...) as upper...
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'.

2 years agoJAL-3628 init log after loading testProps for each backupfile test
Jim Procter [Wed, 5 Aug 2020 16:41:36 +0000 (17:41 +0100)]
JAL-3628 init log after loading testProps for each backupfile test

2 years agoMerge branch 'patch/JAL-3692enaEndpointFlatfile' into releases/Release_2_11_1_Branch
Jim Procter [Wed, 5 Aug 2020 16:29:19 +0000 (17:29 +0100)]
Merge branch 'patch/JAL-3692enaEndpointFlatfile' into releases/Release_2_11_1_Branch

2 years agoJAL-3692 unit test updated for ?gzip download endpoint URL patch/JAL-3692enaEndpointFlatfile
gmungoc [Wed, 5 Aug 2020 16:01:37 +0000 (17:01 +0100)]
JAL-3692 unit test updated for ?gzip download endpoint URL

2 years agoJAL-3692 parse multiline feature qualifiers and escaped quotes
gmungoc [Wed, 5 Aug 2020 15:53:17 +0000 (16:53 +0100)]
JAL-3692 parse multiline feature qualifiers and escaped quotes

2 years agoJAL-3675 release notes for JAL-3477, JAL-3667, JAL-3541, JAL-3685, JAL-3676, JAL...
Jim Procter [Wed, 5 Aug 2020 15:41:48 +0000 (16:41 +0100)]
JAL-3675 release notes for JAL-3477, JAL-3667, JAL-3541, JAL-3685, JAL-3676, JAL-3677 and bumped release date for 2.11.1.1 to next Tuesday(ish)

2 years agoMerge branch 'merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch' into...
Jim Procter [Wed, 5 Aug 2020 14:47:31 +0000 (15:47 +0100)]
Merge branch 'merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch' into releases/Release_2_11_1_Branch

2 years agoJAL-3477 Improved command line arguments description in memory.html
Ben Soares [Tue, 4 Aug 2020 18:30:47 +0000 (19:30 +0100)]
JAL-3477 Improved command line arguments description in memory.html

2 years agoJAL-3477 Added -help text for jvmmempc and jvmmemmax. Fixed typo and slight rewording...
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

2 years agoJAL-3477 added help documentation for executable jar command line arguments -jvmmempc...
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

2 years agoJAL-3675 report JAL-3701 as known defect
Jim Procter [Mon, 3 Aug 2020 13:38:19 +0000 (14:38 +0100)]
JAL-3675 report JAL-3701 as known defect

2 years agoJAL-3675 release notes for JAL-3692
Jim Procter [Mon, 3 Aug 2020 13:10:41 +0000 (14:10 +0100)]
JAL-3675 release notes for JAL-3692

2 years agoMerge branch 'patch/JAL-3692enaEndpointFlatfile' into releases/Release_2_11_1_Branch
Jim Procter [Mon, 3 Aug 2020 12:45:49 +0000 (13:45 +0100)]
Merge branch 'patch/JAL-3692enaEndpointFlatfile' into releases/Release_2_11_1_Branch

2 years agoJAL-3692 fix up test for 2.11.1 series datamodel API
Jim Procter [Mon, 3 Aug 2020 11:06:42 +0000 (12:06 +0100)]
JAL-3692 fix up test for 2.11.1 series datamodel API

2 years agoJAL-3692 set CDS /product as EMBLCDSPROTEIN description
gmungoc [Mon, 27 Jul 2020 15:34:04 +0000 (16:34 +0100)]
JAL-3692 set CDS /product as EMBLCDSPROTEIN description

2 years agoJAL-3692 refactor/complete parsing, more unit test coverage
gmungoc [Mon, 27 Jul 2020 15:26:08 +0000 (16:26 +0100)]
JAL-3692 refactor/complete parsing, more unit test coverage

2 years agoJAL-3692 parse DE for description, and other refactoring...
gmungoc [Fri, 24 Jul 2020 08:38:45 +0000 (09:38 +0100)]
JAL-3692 parse DE for description, and other refactoring...

2 years agoJAL-3692 URL tests updated
gmungoc [Thu, 23 Jul 2020 10:43:32 +0000 (11:43 +0100)]
JAL-3692 URL tests updated

2 years agoJAL-3692 unit test (J03321), fixes, dbrefs; todo: protein mappings
gmungoc [Wed, 22 Jul 2020 09:55:43 +0000 (10:55 +0100)]
JAL-3692 unit test (J03321), fixes, dbrefs; todo: protein mappings

2 years agoJAL-3692 EMBL flatfile fetcher / parser (todo: CDS dbrefs and mappings)
gmungoc [Tue, 21 Jul 2020 11:22:18 +0000 (12:22 +0100)]
JAL-3692 EMBL flatfile fetcher / parser (todo: CDS dbrefs and mappings)
 Conflicts:
src/jalview/ws/dbsources/EmblXmlSource.java
src/jalview/ws/ebi/EBIFetchClient.java

2 years agoMerge branch 'releases/Release_2_11_1_Branch' into bug/JAL-3509hideResnum
Ben Soares [Fri, 31 Jul 2020 16:29:34 +0000 (17:29 +0100)]
Merge branch 'releases/Release_2_11_1_Branch' into bug/JAL-3509hideResnum

2 years agoMerge branch 'bug/JAL-2983negativeSliderMin' into releases/Release_2_11_1_Branch
Jim Procter [Wed, 29 Jul 2020 17:48:52 +0000 (18:48 +0100)]
Merge branch 'bug/JAL-2983negativeSliderMin' into releases/Release_2_11_1_Branch

2 years agoJAL-3371 JAL-2983 don't modify 'extent' of slider - this is managed by look and feel
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

2 years agoJAL-3675 mention -open argument in the command line arguments table
Jim Procter [Wed, 29 Jul 2020 16:46:33 +0000 (17:46 +0100)]
JAL-3675 mention -open argument in the command line arguments table

2 years agoJAL-3675 JAL-3570 JAL-3608 JAL-2983 release notes and docs
Jim Procter [Wed, 29 Jul 2020 16:46:17 +0000 (17:46 +0100)]
JAL-3675 JAL-3570 JAL-3608 JAL-2983 release notes and docs

2 years agoJAL-3675 update release note for JAL-2656
Jim Procter [Tue, 28 Jul 2020 12:43:48 +0000 (13:43 +0100)]
JAL-3675 update release note for JAL-2656

2 years agoJAL-2656 recognise non-HTTP URI input streams as gzipped by detecting the gzip magic...
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

2 years agoJAL-2656 recognise Gzipped file input streams by their content, not their filename
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

2 years agoJAL-3615 update tests for Rfam/Pfam specific gzip endpoints
Jim Procter [Tue, 28 Jul 2020 10:18:56 +0000 (11:18 +0100)]
JAL-3615 update tests for Rfam/Pfam specific gzip endpoints

2 years agoJAL-3675 release notes for JAL-3615 and JAL-2656
Jim Procter [Mon, 27 Jul 2020 18:15:16 +0000 (19:15 +0100)]
JAL-3675 release notes for JAL-3615 and JAL-2656

2 years agoJAL-2656 JAL-3615 check response headers to test for gzipped url reply
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

2 years agoJAL-3615 used gzip endpoints for Pfam and Rfam
gmungoc [Thu, 2 Jul 2020 14:28:36 +0000 (15:28 +0100)]
JAL-3615 used gzip endpoints for Pfam and Rfam
redact parent commits related to JalviewJS for 2.11.1.1 patch

2 years agoMerge branch 'bug/JAL-2983negativeSliderMin' into releases/Release_2_11_1_Branch
Jim Procter [Mon, 27 Jul 2020 15:46:47 +0000 (16:46 +0100)]
Merge branch 'bug/JAL-2983negativeSliderMin' into releases/Release_2_11_1_Branch
Conflict in way transparency slider was inited - followed HEAD's pattern here.

2 years agoJAL-3675 release notes for JAL-3621
Jim Procter [Mon, 27 Jul 2020 15:16:34 +0000 (16:16 +0100)]
JAL-3675 release notes for JAL-3621

2 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

2 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

2 years agoJAL-3675 release notes for JAL-3695 JAL-3696 JAL-3697
Jim Procter [Mon, 27 Jul 2020 14:50:50 +0000 (15:50 +0100)]
JAL-3675 release notes for JAL-3695 JAL-3696 JAL-3697