TZVanaalten [Mon, 7 Aug 2017 15:22:23 +0000 (16:22 +0100)]
JAL-2629 current hmmer commands are now executed in threads
TZVanaalten [Fri, 4 Aug 2017 11:29:11 +0000 (12:29 +0100)]
JAL-2599 fixed information annotation buttons not working
TZVanaalten [Fri, 4 Aug 2017 11:19:51 +0000 (12:19 +0100)]
JAL-2629 hmmbuild now runs on alignments of different lengths
TZVanaalten [Fri, 4 Aug 2017 10:13:17 +0000 (11:13 +0100)]
JAL-2629 multiple HMMs can now be dropped onto an alignment
TZVanaalten [Wed, 2 Aug 2017 12:06:43 +0000 (13:06 +0100)]
JAL-2599 fix for HMM logo not normalising correctly
TZVanaalten [Wed, 2 Aug 2017 09:52:25 +0000 (10:52 +0100)]
JAL-2599 fix issue where parser exported map annotation incorrectly
TZVanaalten [Wed, 2 Aug 2017 09:51:14 +0000 (10:51 +0100)]
JAL-2599 fix for information annotation buttons
TZVanaalten [Mon, 31 Jul 2017 15:24:21 +0000 (16:24 +0100)]
JAL-2629 add hmmalign command
TZVanaalten [Thu, 27 Jul 2017 16:17:08 +0000 (17:17 +0100)]
JAL-2629 implement hmmbuild
TZVanaalten [Thu, 27 Jul 2017 11:06:02 +0000 (12:06 +0100)]
JAL-2629 moved HMM storage location to placeholder sequence
TZVanaalten [Wed, 26 Jul 2017 12:16:48 +0000 (13:16 +0100)]
JAL-2629 HMMs now map to reference annotation if exists
TZVanaalten [Tue, 25 Jul 2017 11:34:26 +0000 (12:34 +0100)]
JAL-2629 add non-functional HMMER menu
TZVanaalten [Tue, 25 Jul 2017 11:28:50 +0000 (12:28 +0100)]
JAL-2616 add ability to perform random alignments within clans
tzvanaalten [Mon, 24 Jul 2017 14:46:18 +0000 (15:46 +0100)]
JAL-2616 add placeholder sequence for HMM, does not yet align properly
tzvanaalten [Mon, 24 Jul 2017 12:44:41 +0000 (13:44 +0100)]
JAL-2616 add ability to change location of family and hmm data
tzvanaalten [Mon, 24 Jul 2017 12:41:09 +0000 (13:41 +0100)]
JAL-2599 add a couple of test files not included in previous commits
tzvanaalten [Mon, 24 Jul 2017 12:40:28 +0000 (13:40 +0100)]
JAL-2616 add test class and test files for analyser
tzvanaalten [Mon, 24 Jul 2017 12:37:14 +0000 (13:37 +0100)]
JAL-2599 .hmm parser should now accept older .hmm files
TZVanaalten [Fri, 21 Jul 2017 13:27:41 +0000 (14:27 +0100)]
JAL-2616 add ability to sort Pfam families and HMMs into clans
TZVanaalten [Thu, 20 Jul 2017 11:42:48 +0000 (12:42 +0100)]
JAL-2616 remove statistical analysis from AlignFrame
TZVanaalten [Thu, 20 Jul 2017 11:07:43 +0000 (12:07 +0100)]
JAL-2599 small code improvements
TZVanaalten [Thu, 20 Jul 2017 11:07:10 +0000 (12:07 +0100)]
JAL-2616 add documentation for probability analyser
TZVanaalten [Thu, 20 Jul 2017 10:45:41 +0000 (11:45 +0100)]
JAL-2616 add probability distribution analyser class
TZVanaalten [Thu, 20 Jul 2017 10:42:11 +0000 (11:42 +0100)]
JAL-2599 add ability to process RNA HMMer files
TZVanaalten [Tue, 18 Jul 2017 11:44:15 +0000 (12:44 +0100)]
JAL-2599 complete documentation for HMM and HMMFile classes
TZVanaalten [Tue, 18 Jul 2017 10:01:18 +0000 (11:01 +0100)]
JAL-2599 modified state transition probability storage
TZVanaalten [Fri, 14 Jul 2017 16:06:08 +0000 (17:06 +0100)]
add partial button fix to annotation and statistics output
TZVanaalten [Wed, 12 Jul 2017 10:05:42 +0000 (11:05 +0100)]
test HMM annotaTION
TZVanaalten [Tue, 11 Jul 2017 13:59:08 +0000 (14:59 +0100)]
complete Information Content annotation
TZVanaalten [Thu, 29 Jun 2017 16:17:28 +0000 (17:17 +0100)]
add information content calculations
TZVanaalten [Thu, 29 Jun 2017 16:16:21 +0000 (17:16 +0100)]
transferred the storage position of the HMM to annotations
TZVanaalten [Fri, 23 Jun 2017 14:19:47 +0000 (15:19 +0100)]
test HMMER colour scheme
TZVanaalten [Fri, 23 Jun 2017 11:52:54 +0000 (12:52 +0100)]
add HMMER colour scheme
TZVanaalten [Thu, 22 Jun 2017 14:01:34 +0000 (15:01 +0100)]
fully integrate HMMER3 file format into Jalview
TZVanaalten [Tue, 20 Jun 2017 16:58:30 +0000 (17:58 +0100)]
create method to test HMM model as string
TZVanaalten [Tue, 20 Jun 2017 16:01:38 +0000 (17:01 +0100)]
restructure file exporter
TZVanaalten [Thu, 15 Jun 2017 11:39:12 +0000 (12:39 +0100)]
add tests for HMMFile class
TZVanaalten [Thu, 15 Jun 2017 11:38:48 +0000 (12:38 +0100)]
add HMMFile class to read and write HMM files
TZVanaalten [Thu, 15 Jun 2017 11:38:03 +0000 (12:38 +0100)]
Update HiddenMarkovModel class
TZVanaalten [Fri, 9 Jun 2017 15:26:39 +0000 (16:26 +0100)]
Add HiddenMarkovModel class
Jim Procter [Wed, 31 May 2017 21:02:55 +0000 (22:02 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 31 May 2017 21:02:41 +0000 (22:02 +0100)]
JAL-2418 release notes for JAL-2547, JAL-2563, JAL-1256
Jim Procter [Wed, 31 May 2017 20:23:52 +0000 (21:23 +0100)]
Merge branch 'JAL-2571' into develop
Jim Procter [Wed, 31 May 2017 20:21:59 +0000 (21:21 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 31 May 2017 20:10:33 +0000 (21:10 +0100)]
JAL-2398 - updated groovy script for direct field modification
Jim Procter [Wed, 31 May 2017 20:07:04 +0000 (21:07 +0100)]
JAL-2418 JAL-2563 release notes
Jim Procter [Wed, 31 May 2017 20:06:31 +0000 (21:06 +0100)]
JAL-2418 typo
Jim Procter [Wed, 31 May 2017 20:05:39 +0000 (21:05 +0100)]
Merge branch 'develop' into documentation/JAL-2418_release2102
tcofoegbu [Wed, 31 May 2017 10:46:22 +0000 (11:46 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Wed, 31 May 2017 10:46:08 +0000 (11:46 +0100)]
JAL-2375 fix unit test to reflect improvement
tcofoegbu [Wed, 31 May 2017 10:08:24 +0000 (11:08 +0100)]
Fixed failing tests
tcofoegbu [Wed, 31 May 2017 09:59:45 +0000 (10:59 +0100)]
JAL-2533 updated unit test to reflect improvement
gmungoc [Wed, 31 May 2017 08:00:46 +0000 (09:00 +0100)]
JAL-2547 handle contact features 'around' a gap correctly
kiramt [Tue, 30 May 2017 18:28:42 +0000 (19:28 +0100)]
JAL-2573 Fixes for alignment < viewport width, and similarly height
gmungoc [Tue, 30 May 2017 15:01:44 +0000 (16:01 +0100)]
JAL-2547 tooltip/AmendFeatures on gap straddled by feature, not for
adjacent feature
kiramt [Tue, 30 May 2017 09:36:34 +0000 (10:36 +0100)]
JAL-2571 Corrected alignment width/height checks to visible only
gmungoc [Tue, 30 May 2017 09:26:46 +0000 (10:26 +0100)]
JAL-2570 don't zap group colour scheme when mapping over split frame
Jim Procter [Mon, 29 May 2017 16:38:34 +0000 (17:38 +0100)]
Merge branch 'bug/JAL-2034contextchange' into develop
Jim Procter [Mon, 29 May 2017 16:35:35 +0000 (17:35 +0100)]
JAL-2388 release notes
Jim Procter [Mon, 29 May 2017 14:00:18 +0000 (15:00 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Mon, 29 May 2017 13:58:33 +0000 (14:58 +0100)]
JAL-2520 properly documented as a fixed bug in release notes
Jim Procter [Mon, 29 May 2017 13:26:21 +0000 (14:26 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Mon, 29 May 2017 13:25:40 +0000 (14:25 +0100)]
JAL-2465,JAL-2520,JAL-2533 release notes
Jim Procter [Mon, 29 May 2017 13:19:41 +0000 (14:19 +0100)]
Merge branch 'features/JAL-2465_No-mapping_Jmol-structures-loaded-via-url' into develop
Jim Procter [Mon, 29 May 2017 13:07:47 +0000 (14:07 +0100)]
JAL-2533 update javadoc
Jim Procter [Mon, 29 May 2017 12:51:59 +0000 (13:51 +0100)]
JAL-2465 fixed groups for JmolViewerTest.testStructureLoadingViaURL
Jim Procter [Mon, 29 May 2017 11:18:53 +0000 (12:18 +0100)]
Merge branch 'bug/JAL-2536' into develop
Jim Procter [Mon, 29 May 2017 11:18:09 +0000 (12:18 +0100)]
JAL-2536 tweak javadoc wording
Jim Procter [Mon, 29 May 2017 11:10:54 +0000 (12:10 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Mon, 29 May 2017 11:10:33 +0000 (12:10 +0100)]
JAL-2517 release notes
Jim Procter [Mon, 29 May 2017 10:52:46 +0000 (11:52 +0100)]
Merge branch 'bug/JAL-2517cancelAppletColour' into develop
Jim Procter [Mon, 29 May 2017 10:50:01 +0000 (11:50 +0100)]
release notes
JAL-2550 known defect
JAL-2535 stockholm->PP annotation
Jim Procter [Mon, 29 May 2017 10:01:19 +0000 (11:01 +0100)]
JAL-2418 updated JABAWS server in what’s new
Jim Procter [Mon, 29 May 2017 10:00:56 +0000 (11:00 +0100)]
JAL-2491 JAL-2526 JAL-2566 JAL-2563 JAL-2547 release notes
Jim Procter [Sat, 27 May 2017 13:16:18 +0000 (14:16 +0100)]
Merge branch 'bug/JAL-2491' into develop
Jim Procter [Sat, 27 May 2017 13:02:54 +0000 (14:02 +0100)]
Merge branch 'bug/JAL-2547tooltipOnGap' into develop
Jim Procter [Sat, 27 May 2017 13:01:59 +0000 (14:01 +0100)]
Merge branch 'task/JAL-2562_SequenceI.findPosition' into develop
Jim Procter [Sat, 27 May 2017 13:01:41 +0000 (14:01 +0100)]
JAL-2563 failing test to verify SetStatus returns position and message includes the position for ambiguous peptide ‘B’.
Jim Procter [Sat, 27 May 2017 13:00:49 +0000 (14:00 +0100)]
JAL-2563 test to verify SetStatus returns -1 so mouseOver events are raised via StructureSelectionManager (JAL-2491, expected fixed by JAL-2547)
Jim Procter [Sat, 27 May 2017 11:58:30 +0000 (12:58 +0100)]
Merge branch 'task/JAL-2562_SequenceI.findPosition' into develop
Jim Procter [Sat, 27 May 2017 11:57:37 +0000 (12:57 +0100)]
JAL-2547 JAL-2562 rejig SetStatusMessage return value test for legibility and maximum assert coverage before JAL-2526 causes failure
Jim Procter [Sat, 27 May 2017 11:41:43 +0000 (12:41 +0100)]
Merge branch 'task/JAL-2562_SequenceI.findPosition' into develop
Jim Procter [Sat, 27 May 2017 11:32:09 +0000 (12:32 +0100)]
JAL-2526 test and documentation for SeqPanel.setStatus behaviour needed to fix bug noted on JAL-2491 where mouseover at gap highlights position for sequence to right of gap in complementary view.
Jim Procter [Sat, 27 May 2017 10:25:02 +0000 (11:25 +0100)]
JAL-2562 javadoc TODO
kiramt [Fri, 26 May 2017 21:11:00 +0000 (22:11 +0100)]
JAL-2491 Missed port to applet from JAL-1691
Jim Procter [Fri, 26 May 2017 16:37:57 +0000 (17:37 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Fri, 26 May 2017 16:37:31 +0000 (17:37 +0100)]
JAL-2418 updated JPred documentation and screenshot for JPred4
Jim Procter [Fri, 26 May 2017 16:37:07 +0000 (17:37 +0100)]
JAL-2418 JAL-2549 JABAWS 2.2 release notes
Jim Procter [Fri, 26 May 2017 15:29:20 +0000 (16:29 +0100)]
Merge branch 'features/JAL-2549_updateJABAWSto220' into develop
tcofoegbu [Fri, 26 May 2017 14:27:16 +0000 (15:27 +0100)]
JAL-2465 Improvement to re-instate storing recently opened URLs for alignments loaded from a structure format via URL
tcofoegbu [Fri, 26 May 2017 13:48:44 +0000 (14:48 +0100)]
JAL-2465 fix to prevent files loaded from the system's temporary directory from being included in recently opend files store
kiramt [Thu, 25 May 2017 13:31:51 +0000 (14:31 +0100)]
JAl-2034 Ported to applet
kiramt [Thu, 25 May 2017 13:06:38 +0000 (14:06 +0100)]
JAL-2034 don't update overview after click without drag on group
kiramt [Thu, 25 May 2017 07:49:08 +0000 (08:49 +0100)]
Merge branch 'bug/JAL-2551' into bug/JAL-2034contextchange
kiramt [Wed, 24 May 2017 12:47:58 +0000 (13:47 +0100)]
JAL-2551 Fix to group colouring when group extent is reduced
kiramt [Wed, 24 May 2017 09:44:47 +0000 (10:44 +0100)]
JAL-2034 Added isDefined flag to SequenceGroup
Jim Procter [Tue, 23 May 2017 19:39:17 +0000 (20:39 +0100)]
JAL-2549 RNAAliFold result to annotation file roundtrip test fails test due to JAL-2550 - Upper/lower case alphabet recognised as WUSS RNA annotation
Jim Procter [Tue, 23 May 2017 19:35:59 +0000 (20:35 +0100)]
JAL-2549 skip ‘Unrecognised Service’ which resolves to a null entry in the get supported services list
Jim Procter [Tue, 23 May 2017 19:35:23 +0000 (20:35 +0100)]
JAL-2549 replace JABAWS 2.1 with 2.2 client and remove JPredWS client and tests
gmungoc [Tue, 23 May 2017 11:55:08 +0000 (12:55 +0100)]
JAL-2547 don't show features in tooltip over a gap
git://source.jalview.org / jalview.git / log