Jim Procter [Tue, 14 Apr 2020 15:33:22 +0000 (16:33 +0100)]
JAL-3529 revert ordering of DBRef addition so it reflects situation after Pfam import </picky>
Ben Soares [Fri, 6 Mar 2020 10:33:42 +0000 (10:33 +0000)]
JAL-3529 improved regex in Stockholm UNIPROT accession id test
Jim Procter [Tue, 18 Feb 2020 18:38:12 +0000 (18:38 +0000)]
JAL-3529 attempt to guess database for a sequence’s AC record based on the sequence type if the alignment had no PFAM or RFAM accession
Jim Procter [Tue, 18 Feb 2020 18:37:39 +0000 (18:37 +0000)]
JAL-3529 test for AC <Uniprot/EMBL> rather than DR in Stockholm file
Jim Procter [Tue, 18 Feb 2020 17:40:12 +0000 (17:40 +0000)]
JAL-3529 assert Uniprot refs must be provided as primary ‘AC’ ref
Jim Procter [Fri, 14 Feb 2020 16:06:56 +0000 (16:06 +0000)]
JAL-3532 TODO comment
Jim Procter [Fri, 14 Feb 2020 14:43:06 +0000 (14:43 +0000)]
fix for JAL-3529
Jim Procter [Fri, 14 Feb 2020 14:40:10 +0000 (14:40 +0000)]
JAL-3531 failing test
Jim Procter [Fri, 14 Feb 2020 14:27:46 +0000 (14:27 +0000)]
JAL-3529 more detailed asserts to detect whitespace in DBRefs imported from Stockholm
Jim Procter [Fri, 14 Feb 2020 14:27:03 +0000 (14:27 +0000)]
JAL-3529 preferentially output source dbrefs or principle db for sequence type before others.
Jim Procter [Fri, 14 Feb 2020 13:49:02 +0000 (13:49 +0000)]
JAL-3529 failing test for bug
Ben Soares [Wed, 12 Feb 2020 12:18:27 +0000 (12:18 +0000)]
JAL-3289 Updated doc/building.md to explain possible values of the CHANNEL property during building
Jim Procter [Tue, 11 Feb 2020 16:52:21 +0000 (16:52 +0000)]
JAL-3407 release notes for JAL-3375
Jim Procter [Tue, 11 Feb 2020 12:14:10 +0000 (12:14 +0000)]
JAL-3376 highlighted in what’s new
Jim Procter [Tue, 11 Feb 2020 12:13:41 +0000 (12:13 +0000)]
JAL-3407 - JAL-3376 JAL-3377 release notes
Jim Procter [Tue, 11 Feb 2020 12:13:05 +0000 (12:13 +0000)]
JAL-3407 start of whats new for 2.11.1.0
Jim Procter [Tue, 11 Feb 2020 12:11:37 +0000 (12:11 +0000)]
JAL-3376 documentation for standard attributes for variants from VCF
Jim Procter [Tue, 11 Feb 2020 10:38:31 +0000 (10:38 +0000)]
JAL-3407 release notes (JAL-3386 signoff, new-knowns JAL-3523 JAL-3525)
Jim Procter [Mon, 10 Feb 2020 17:08:05 +0000 (17:08 +0000)]
JAL-3407 JAL-3508 move to 2.11.1.0 point release versioning and signed off JAL-3510 JAL-3513 JAL-3388 JAL-3389 JAL-3441 JAL-3473 JAL-3406
Jim Procter [Mon, 3 Feb 2020 16:42:42 +0000 (16:42 +0000)]
Merge branch 'task/JAL-3510-update-clover-to-4.4.1' into develop
fix JAL-3513 and fixes/resolves JAL-3510
Jim Procter [Mon, 3 Feb 2020 16:24:59 +0000 (16:24 +0000)]
JAL-3510 JAL-3153 clover instrumentation for tests
Jim Procter [Thu, 30 Jan 2020 08:44:47 +0000 (08:44 +0000)]
JAL-3510 bump clover version in gradle build dependencies
Ben Soares [Wed, 29 Jan 2020 16:20:24 +0000 (16:20 +0000)]
JAL-3341 Increase number of lines looked at by test. Fixes two tests
gmungoc [Tue, 28 Jan 2020 15:18:12 +0000 (15:18 +0000)]
JAL-3341 debug for failing unit test
gmungoc [Tue, 28 Jan 2020 12:30:07 +0000 (12:30 +0000)]
Merge branch 'feature/JAL-3121gffAttributeMap' into develop
gmungoc [Thu, 22 Aug 2019 08:06:23 +0000 (09:06 +0100)]
JAL-3187 one more obsolete method removed
gmungoc [Fri, 24 Jan 2020 10:41:11 +0000 (10:41 +0000)]
JAL=3121 more data format validation/tests, help text tweak
gmungoc [Thu, 23 Jan 2020 17:19:03 +0000 (17:19 +0000)]
JAL-3121 update help page for GFF column 9 nested attributes
gmungoc [Thu, 23 Jan 2020 16:22:39 +0000 (16:22 +0000)]
JAL-3121 'attributes map' in GFF3 without special 'jvmap_' token
Jim Procter [Thu, 16 Jan 2020 14:38:45 +0000 (14:38 +0000)]
JAL-3474 release notes
Jim Procter [Thu, 16 Jan 2020 14:30:31 +0000 (14:30 +0000)]
Merge branch 'improvement/JAL-3474_lots_of_.cvsignore_files' into develop
Ben Soares [Thu, 31 Oct 2019 14:18:48 +0000 (14:18 +0000)]
JAL-3473 Checked value of def and min. Set def to min if lower than min.
Jim Procter [Thu, 12 Dec 2019 15:20:07 +0000 (15:20 +0000)]
JAL-2305 moved failing CrossRef tests to Functional_Failing group
Jim Procter [Thu, 12 Dec 2019 14:48:40 +0000 (14:48 +0000)]
JAL-3407 update release date for Jalview 2.11.1
Ben Soares [Fri, 1 Nov 2019 15:21:35 +0000 (15:21 +0000)]
JAL-3474 removed all .cvsignore files stored in the repo
Jim Procter [Tue, 15 Oct 2019 15:11:07 +0000 (16:11 +0100)]
JAL-3407 update release date for Jalview 2.11.1
Jim Procter [Fri, 11 Oct 2019 10:00:30 +0000 (11:00 +0100)]
Merge branch 'develop' into documentation/JAL-3407_2.11.1_release
gmungoc [Thu, 26 Sep 2019 14:42:09 +0000 (15:42 +0100)]
JAL-2481 remove code duplication left by merge
gmungoc [Thu, 26 Sep 2019 13:59:23 +0000 (14:59 +0100)]
JAL-3441 action double-click in Feature Type column only
gmungoc [Fri, 23 Aug 2019 14:38:29 +0000 (15:38 +0100)]
JAL-3141 correct cast of spinner value
gmungoc [Thu, 22 Aug 2019 16:26:53 +0000 (17:26 +0100)]
JAL-3121 slightly cleaner parsing of, and unit test for, map attributes
gmungoc [Thu, 22 Aug 2019 15:06:36 +0000 (16:06 +0100)]
Merge branch 'develop' into feature/JAL-3121gffAttributeMap
gmungoc [Thu, 22 Aug 2019 15:06:05 +0000 (16:06 +0100)]
JAL-3187 case-insensitive codon variant calculation
gmungoc [Thu, 22 Aug 2019 14:48:38 +0000 (15:48 +0100)]
JAL-3121 round trip GFF attributes including map-valued attributes
gmungoc [Thu, 22 Aug 2019 08:06:23 +0000 (09:06 +0100)]
JAL-3187 one more obsolete method removed
gmungoc [Wed, 21 Aug 2019 16:01:52 +0000 (17:01 +0100)]
JAL-3187 minor code tidying, todo removal
Jim Procter [Mon, 12 Aug 2019 15:35:36 +0000 (16:35 +0100)]
JAL-2987 release notes
Jim Procter [Mon, 12 Aug 2019 14:15:03 +0000 (15:15 +0100)]
JAL-3407 update RELEASE and cut new release notes in releaseHistory.html
Jim Procter [Mon, 12 Aug 2019 13:54:19 +0000 (14:54 +0100)]
JAL-3407 JAL-3406 update credits in Jalview 2.11.1
gmungoc [Fri, 9 Aug 2019 08:01:10 +0000 (09:01 +0100)]
JAL-3187 removal of variant feature (non-virtual) transfer to protein
gmungoc [Wed, 7 Aug 2019 09:25:09 +0000 (10:25 +0100)]
JAL-3187 (fudge) look in both alignments for stored mappings
gmungoc [Wed, 7 Aug 2019 08:42:01 +0000 (09:42 +0100)]
Merge branch 'develop' into feature/JAL-3187linkedFeatures
gmungoc [Wed, 31 Jul 2019 11:59:39 +0000 (12:59 +0100)]
JAL-3389 add .py to restored Chimera session filename so it opens!
gmungoc [Wed, 31 Jul 2019 08:10:11 +0000 (09:10 +0100)]
Merge branch 'bug/JAL-3388structureChooserSorting' into develop
gmungoc [Tue, 30 Jul 2019 17:45:21 +0000 (18:45 +0100)]
JAL-3198 more efficient Sequence.getDisplayId()
gmungoc [Tue, 30 Jul 2019 16:51:13 +0000 (17:51 +0100)]
JAL-3388 correct class for column 0 Ref Sequence
gmungoc [Mon, 29 Jul 2019 14:48:30 +0000 (15:48 +0100)]
JAL-3386 correct wrapped width calculation for headless image export
gmungoc [Mon, 29 Jul 2019 14:35:22 +0000 (15:35 +0100)]
JAL-3377 more reused of SeqCanvas.computeWrappedGeometry
gmungoc [Mon, 29 Jul 2019 10:44:06 +0000 (11:44 +0100)]
JAL-3377 add seq-annotations gap to cheight not to hgap
gmungoc [Mon, 29 Jul 2019 10:34:05 +0000 (11:34 +0100)]
JAL-3377 Javadoc added for getWrappedHeight()
gmungoc [Sun, 28 Jul 2019 10:05:32 +0000 (11:05 +0100)]
JAL-3377 corrected wrapped widths height for IdCanvas
gmungoc [Mon, 29 Jul 2019 10:20:44 +0000 (11:20 +0100)]
JAL-3377 include seq-annotation spacing in getWrappedHeight()
gmungoc [Fri, 26 Jul 2019 18:42:30 +0000 (20:42 +0200)]
Merge branch 'features/JAL-3375vcfValidation' into
feature/JAL-3187linkedFeatures
Conflicts:
src/jalview/io/vcf/VCFLoader.java
test/jalview/io/vcf/VCFLoaderTest.java
gmungoc [Fri, 26 Jul 2019 16:52:01 +0000 (18:52 +0200)]
JAL-1793 only decode specific special characters in VCF data
gmungoc [Fri, 26 Jul 2019 15:58:06 +0000 (17:58 +0200)]
JAL-3376 capture VCF POS, ID, QUAL, FILTER as feature attributes
gmungoc [Fri, 26 Jul 2019 13:40:28 +0000 (15:40 +0200)]
JAL-3375 format validate VCF Integer and Float fields
gmungoc [Thu, 25 Jul 2019 10:48:33 +0000 (12:48 +0200)]
JAL-3375 ignore '.' values for VCF data
gmungoc [Tue, 16 Jul 2019 16:13:19 +0000 (17:13 +0100)]
Merge branch 'develop' into feature/JAL-3187linkedFeatures
gmungoc [Tue, 16 Jul 2019 10:23:35 +0000 (11:23 +0100)]
JAL-2987 tolerate null double values when formatting JTable
gmungoc [Wed, 10 Jul 2019 16:03:42 +0000 (17:03 +0100)]
Merge branch 'develop' into feature/JAL-3187linkedFeatures
Jim Procter [Wed, 10 Jul 2019 13:09:18 +0000 (14:09 +0100)]
JAL-3289 bamboo properties for ‘BUILD’ getdown channel - fix
Jim Procter [Wed, 10 Jul 2019 12:55:56 +0000 (13:55 +0100)]
JAL-3289 bamboo properties for ‘BUILD’ getdown channel
gmungoc [Mon, 8 Jul 2019 10:47:06 +0000 (11:47 +0100)]
JAL-3187 derived peptide variants tweaks and tests
gmungoc [Fri, 5 Jul 2019 10:44:14 +0000 (11:44 +0100)]
JAL-3187 initial refactoring towards peptide variant in tooltip
Ben Soares [Fri, 5 Jul 2019 09:43:30 +0000 (10:43 +0100)]
JAL-1544 fixed a html encoding of '<' (%lt; -> <) in commandline.html
gmungoc [Fri, 5 Jul 2019 09:09:12 +0000 (10:09 +0100)]
JAL-1793 apply URL decoding when saving VCF attribute values (%3D -> =)
Jim Procter [Thu, 4 Jul 2019 15:40:13 +0000 (16:40 +0100)]
JAL-3111 correct JVL appbase for 2.10.5 via getdown
Jim Procter [Thu, 4 Jul 2019 15:34:12 +0000 (16:34 +0100)]
Merge branch 'task/JAL-3337-rm-lib-update-sourceDist' into develop
Jim Procter [Thu, 4 Jul 2019 15:33:48 +0000 (16:33 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Thu, 4 Jul 2019 15:31:47 +0000 (16:31 +0100)]
JAL-3337 round-and-round the process source files again
Jim Procter [Thu, 4 Jul 2019 15:23:16 +0000 (16:23 +0100)]
JAL-3337 more includes and excludes
Jim Procter [Thu, 4 Jul 2019 14:52:05 +0000 (15:52 +0100)]
JAL-3337 remove the old lib directory !
Jim Procter [Thu, 4 Jul 2019 14:51:28 +0000 (15:51 +0100)]
JAL-3337 rejig the source distribution generation to process and replace tokens in source files
Jim Procter [Thu, 4 Jul 2019 14:36:07 +0000 (15:36 +0100)]
JAL-3111 replace year in header for help pages and put processed help in build/distributions
Ben Soares [Thu, 4 Jul 2019 13:43:47 +0000 (14:43 +0100)]
JAL-3225 try/catch for non-deprecated/deprecated property in sourceDist which is not available on older eclipses
Ben Soares [Thu, 4 Jul 2019 13:16:14 +0000 (14:16 +0100)]
JAL-3353 Change to build.gradle to use the file:// enabled getdown-launcher-local.jar for LOCAL and ARCHIVELOCAL builds only. Otherwise the getdown-launcher.jar (with no local file enabled) will be used
gmungoc [Thu, 4 Jul 2019 12:09:21 +0000 (13:09 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Thu, 4 Jul 2019 12:09:13 +0000 (13:09 +0100)]
JAL-3111 help pages minor corrections
Ben Soares [Thu, 4 Jul 2019 11:26:37 +0000 (12:26 +0100)]
JAL-3348 fixed an internal href in help to allow building
Ben Soares [Thu, 4 Jul 2019 11:25:43 +0000 (12:25 +0100)]
JAL-3337 adjusted building doc as sourceDist uses gradle 5.2 or above properties
Jim Procter [Thu, 4 Jul 2019 08:08:21 +0000 (09:08 +0100)]
Merge branch 'task/JAL-3348_document_cli_memory_settings_when_launching_jalview' into develop
Jim Procter [Thu, 4 Jul 2019 08:05:12 +0000 (09:05 +0100)]
JAL-3111 JAL-3348 JVL file documentation
Jim Procter [Thu, 4 Jul 2019 07:36:42 +0000 (08:36 +0100)]
JAL-3348 revised bsoares memory settings documentation and updated docs for launching jalview from command line
Ben Soares [Thu, 4 Jul 2019 00:04:51 +0000 (01:04 +0100)]
Merge branch 'develop' into task/JAL-3348_document_cli_memory_settings_when_launching_jalview
merging in develop
Ben Soares [Wed, 3 Jul 2019 23:59:39 +0000 (00:59 +0100)]
JAL-3348 memory.html documentation finished for 2.11.0
Ben Soares [Wed, 3 Jul 2019 22:42:35 +0000 (23:42 +0100)]
JAL-3348 jvmmempc in jvl file now works in linux
Ben Soares [Wed, 3 Jul 2019 22:14:41 +0000 (23:14 +0100)]
JAL-3348 jvmmempc multiple values shouldn't be merged
Jim Procter [Wed, 3 Jul 2019 19:58:37 +0000 (20:58 +0100)]
JAL-3111 tidy up lists/indentation for release notes
Jim Procter [Wed, 3 Jul 2019 17:36:25 +0000 (18:36 +0100)]
JAL-3111 Java 11 only and 'onwards'
Jim Procter [Wed, 3 Jul 2019 17:35:15 +0000 (18:35 +0100)]
JAL-3111 more whatsNew tweaks
git://source.jalview.org / jalview.git / log