Jim Procter [Tue, 13 Aug 2019 15:22:01 +0000 (16:22 +0100)]
Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into merge-212
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
Jim Procter [Mon, 15 Jul 2019 16:21:05 +0000 (17:21 +0100)]
Merge branch 'merge/JAL-3285_mchmmer_with_211_develop' into alpha/JAL-3362_Jalview_212_alpha
Thomas [Fri, 12 Jul 2019 14:46:32 +0000 (15:46 +0100)]
JAL-2629 can now choose number of jackhmmer iterations
Thomas [Fri, 12 Jul 2019 13:44:44 +0000 (14:44 +0100)]
JAL-2629 fix faulty label in a MessageManager.getString() call
Thomas [Fri, 12 Jul 2019 13:43:55 +0000 (14:43 +0100)]
JAL-2629 add sort by evalue and bit score
Thomas [Fri, 12 Jul 2019 13:42:48 +0000 (14:42 +0100)]
JAL-2629 hmmer searches now read domain rather than full scores
Jim Procter [Thu, 11 Jul 2019 15:59:28 +0000 (16:59 +0100)]
Merge branch 'merge/JAL-3285_mchmmer_with_211_develop' into alpha/JAL-3362_Jalview_212_alpha
Thomas [Thu, 11 Jul 2019 14:11:52 +0000 (15:11 +0100)]
JAL-2629 hmmer searches include seqs past inclusion threshold in output
Thomas [Thu, 11 Jul 2019 13:47:42 +0000 (14:47 +0100)]
JAL-2629 hmm search UI and structural improvements, inclusion thresholds
Jim Procter [Wed, 10 Jul 2019 16:46:23 +0000 (17:46 +0100)]
JAL-3070 standard way of storing/recovering documentation URL for service
Jim Procter [Wed, 10 Jul 2019 16:33:25 +0000 (17:33 +0100)]
JAL-3070 remove final reference to Jws2Instance
gmungoc [Wed, 10 Jul 2019 16:03:42 +0000 (17:03 +0100)]
Merge branch 'develop' into feature/JAL-3187linkedFeatures
tva [Wed, 10 Jul 2019 15:49:50 +0000 (16:49 +0100)]
JAL-2629 fix hmmsearch/jackhmmer assigning incorrect evalues and scores
Jim Procter [Wed, 10 Jul 2019 14:53:07 +0000 (15:53 +0100)]
Merge branch 'tasks/JAL-3070_wsinterfaces' into alpha/JAL-3362_Jalview_212_alpha
tva [Wed, 10 Jul 2019 14:39:41 +0000 (15:39 +0100)]
JAL-2629 fix hmsearch and jackhmmer not being able to search alignment
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
tva [Wed, 10 Jul 2019 14:12:58 +0000 (15:12 +0100)]
JAL-2629 hmmsearch # of new sequences now only displayed when specified
tva [Wed, 10 Jul 2019 13:41:40 +0000 (14:41 +0100)]
JAL-2629 fix incorrect hmmbuild on groups behaviour
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
Jim Procter [Wed, 10 Jul 2019 12:05:46 +0000 (13:05 +0100)]
Merge branch 'merge/JAL-3285_mchmmer_with_211_develop' into alpha/JAL-3362_Jalview_212_alpha
tva [Wed, 10 Jul 2019 12:05:12 +0000 (13:05 +0100)]
JAL-2629 fix hmmsearch/jackhmmer being unable to search through DB file
gmungoc [Mon, 8 Jul 2019 10:47:06 +0000 (11:47 +0100)]
JAL-3187 derived peptide variants tweaks and tests
tva [Fri, 5 Jul 2019 14:59:00 +0000 (15:59 +0100)]
JAL-2629 uniquify all hmmer command sequence outputs
gmungoc [Fri, 5 Jul 2019 10:44:14 +0000 (11:44 +0100)]
JAL-3187 initial refactoring towards peptide variant in tooltip
tva [Fri, 5 Jul 2019 09:58:52 +0000 (10:58 +0100)]
JAL-2629 fix file format issues preventing hmmsearch, jackhmmer running
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
Jim Procter [Wed, 3 Jul 2019 17:06:46 +0000 (18:06 +0100)]
Merge branch 'task/JAL-3337_gradle_tasks_sourceDist_and_help2Website' into develop
Jim Procter [Wed, 3 Jul 2019 17:05:14 +0000 (18:05 +0100)]
JAL-3111 more whats new
Ben Soares [Wed, 3 Jul 2019 16:24:57 +0000 (17:24 +0100)]
JAL-3348 start of new memory setting text
Ben Soares [Wed, 3 Jul 2019 16:06:55 +0000 (17:06 +0100)]
JAL-3348 jvmmempc allowed in jvl file
Ben Soares [Wed, 3 Jul 2019 15:24:54 +0000 (16:24 +0100)]
Merge branch 'develop' into task/JAL-3348_document_cli_memory_settings_when_launching_jalview
merging in develop
Jim Procter [Wed, 3 Jul 2019 12:58:20 +0000 (13:58 +0100)]
Merge branch 'documentation/JAL-2843_featureFiltersFormat' into develop
tva [Wed, 3 Jul 2019 12:45:22 +0000 (13:45 +0100)]
JAL-2629 fix search scores being read in incorrectly
tva [Wed, 3 Jul 2019 12:44:36 +0000 (13:44 +0100)]
JAL-2629 fix hmm on alignment being deleted upon running jackhmmer
tva [Wed, 3 Jul 2019 11:16:50 +0000 (12:16 +0100)]
JAL-2629 evalues and bit scores now conserved after hmmalign is run
tva [Wed, 3 Jul 2019 10:12:48 +0000 (11:12 +0100)]
JAL-2629 removed empty line produced under sequence report
tva [Wed, 3 Jul 2019 10:07:33 +0000 (11:07 +0100)]
JAL-2629 can now filter by sequence e-value or bit score
Ben Soares [Wed, 3 Jul 2019 00:36:50 +0000 (01:36 +0100)]
JAL-3348 prepping getdown to pass JVM command line args
Jim Procter [Tue, 2 Jul 2019 22:35:18 +0000 (23:35 +0100)]
JAL-3111 updated what’s new… still more to come !
Jim Procter [Tue, 2 Jul 2019 22:34:46 +0000 (23:34 +0100)]
JAL-3111 updated privacy statement to remove mention of JNLP version checker JAL-3280
Jim Procter [Tue, 2 Jul 2019 22:30:52 +0000 (23:30 +0100)]
JAL-3111 JAL-3150 revised Jalview archive documentation and noted instructions about converting Jalview project files pre Jalview 2.1.
Jim Procter [Tue, 2 Jul 2019 22:20:04 +0000 (23:20 +0100)]
JAL-3111 JAL-3348 removed pre 2.11 instructions on setting Jalview’s memory settings. Needs information about configuring proportion of memory allocated.
Jim Procter [Tue, 2 Jul 2019 22:18:13 +0000 (23:18 +0100)]
JAL-3111 JAL-3280 hide the version check preference option in ‘Connections’ tab
Jim Procter [Tue, 2 Jul 2019 22:11:00 +0000 (23:11 +0100)]
JAL-3111 tidied up preferences dialog documentation
Jim Procter [Tue, 2 Jul 2019 20:21:09 +0000 (21:21 +0100)]
JAL-3111 fix broken helpTOC link
Jim Procter [Tue, 2 Jul 2019 20:19:46 +0000 (21:19 +0100)]
Merge branch 'tasks/JAL-3311_removeVamsasMenu' into develop
Jim Procter [Tue, 2 Jul 2019 19:47:52 +0000 (20:47 +0100)]
Merge branch 'develop' into tasks/JAL-3311_removeVamsasMenu
Ben Soares [Tue, 2 Jul 2019 19:26:50 +0000 (20:26 +0100)]
Merge branch 'develop' into task/JAL-3337_gradle_tasks_sourceDist_and_help2Website
merging in develop
Ben Soares [Tue, 2 Jul 2019 19:16:01 +0000 (20:16 +0100)]
JAL-3337 Tidied up j8libs in THIRDPARTYLIBS. Replaced jersey-*-1.19.jar with jersey-*-1.19.4.jar in j8lib. Removed lib/ folder from sourceDist. Added instructions for running testNG with a specific group of tests to building.md
Jim Procter [Tue, 2 Jul 2019 15:06:55 +0000 (16:06 +0100)]
JAL-3111 release date now 4th July 2019 - codename 'bastille'
Jim Procter [Tue, 2 Jul 2019 14:34:10 +0000 (15:34 +0100)]
Merge branch 'documentation/JAL-3111_release_211' into develop
Jim Procter [Tue, 2 Jul 2019 14:33:20 +0000 (15:33 +0100)]
JAL-3111 formatting
Jim Procter [Tue, 2 Jul 2019 14:32:53 +0000 (15:32 +0100)]
JAL-3111 new known defect from JAL-797
git://source.jalview.org / jalview.git / log