gmungoc [Mon, 14 May 2018 13:19:31 +0000 (14:19 +0100)]
JAL-2989 refactoring to reduce code duplication
gmungoc [Mon, 14 May 2018 11:17:51 +0000 (12:17 +0100)]
JAL-2711 show short file names in search database combo box
gmungoc [Mon, 14 May 2018 11:17:18 +0000 (12:17 +0100)]
JAL-2989 support value display names for Option or Parameters combo boxes
gmungoc [Mon, 14 May 2018 10:47:12 +0000 (11:47 +0100)]
JAL-2711 removed unused and flaky utility method
gmungoc [Mon, 14 May 2018 08:17:37 +0000 (09:17 +0100)]
JAL-2939 check for hmm present when processing groups
gmungoc [Fri, 11 May 2018 15:34:35 +0000 (16:34 +0100)]
JAL-2985 show label instead of checkbox for a required (Jalview) Option
gmungoc [Fri, 11 May 2018 11:25:16 +0000 (12:25 +0100)]
Merge branch 'develop' into features/mchmmer
gmungoc [Fri, 11 May 2018 11:19:52 +0000 (12:19 +0100)]
JAL-2986 corrected findIndex for out of range residue value
gmungoc [Fri, 11 May 2018 11:17:18 +0000 (12:17 +0100)]
JAL-2986 additional asserts for SequenceCursor updates
gmungoc [Fri, 11 May 2018 10:57:56 +0000 (11:57 +0100)]
JAL-2986 failing test added
gmungoc [Thu, 10 May 2018 14:30:43 +0000 (15:30 +0100)]
JAL-2629 revert to showing Profile parameter even if only 1 choice
gmungoc [Thu, 10 May 2018 14:17:53 +0000 (15:17 +0100)]
JAL-2629 default HMMBuild to alignment if not specified by args
gmungoc [Thu, 10 May 2018 14:17:20 +0000 (15:17 +0100)]
JAL-591 reduced updating by checking/setting 'updating' flag
gmungoc [Thu, 10 May 2018 12:34:59 +0000 (13:34 +0100)]
JAL-2629 handle decline 'Add Database'
gmungoc [Thu, 10 May 2018 12:34:37 +0000 (13:34 +0100)]
JAL-2629 adjust placement and optionality of arguments/options
gmungoc [Thu, 10 May 2018 12:33:25 +0000 (13:33 +0100)]
JAL-591 show choice list with a single option
Jim Procter [Thu, 10 May 2018 10:49:14 +0000 (11:49 +0100)]
JAL-2920 release notes
Jim Procter [Thu, 10 May 2018 10:35:44 +0000 (11:35 +0100)]
Merge branch 'bug/JAL-2920_uniprotvariantfeature' into releases/Release_2_10_4_Branch
Jim Procter [Thu, 10 May 2018 10:35:11 +0000 (11:35 +0100)]
JAL-2920 basic test for Description from features with/out description, variation and original attributes
Jim Procter [Thu, 10 May 2018 10:34:23 +0000 (11:34 +0100)]
JAL-2920 simplified logic and added corner cases for missing attributes (probably not needed but..)
Jim Procter [Wed, 9 May 2018 19:46:50 +0000 (20:46 +0100)]
JAL-2906 update release date and release notes
Jim Procter [Wed, 9 May 2018 19:46:04 +0000 (20:46 +0100)]
JAL-2931 patch IA paths for new build box
gmungoc [Wed, 9 May 2018 15:57:00 +0000 (16:57 +0100)]
JAL-2714 HMMSearch cutoff by E-Value, Score or None
gmungoc [Wed, 9 May 2018 13:59:14 +0000 (14:59 +0100)]
JAL-2984 add pdb as sequence(s) if associate structure is declined
Jim Procter [Wed, 9 May 2018 09:39:51 +0000 (10:39 +0100)]
Merge branch 'patch/JAL-2976_vaqua4_fallback' into releases/Release_2_10_4_Branch
Jim Procter [Wed, 9 May 2018 09:39:19 +0000 (10:39 +0100)]
JAL-2976 fixed bad equivalence check and implemented belt-and-braces check for quaqua in class name string of look and feel to decide when to fallback to violetlib-Aqua.
Jim Procter [Tue, 8 May 2018 09:59:37 +0000 (10:59 +0100)]
JAL-2321 release notes
Jim Procter [Tue, 8 May 2018 09:57:35 +0000 (10:57 +0100)]
Merge branch 'patch/JAL-2321_addsecstrForDroppedPDBFile' into releases/Release_2_10_4_Branch
gmungoc [Tue, 8 May 2018 09:33:48 +0000 (10:33 +0100)]
Merge branch 'develop' into features/mchmmer
Jim Procter [Mon, 7 May 2018 17:08:38 +0000 (18:08 +0100)]
JAL-2321 patch test to ensure structures are actually annotated when loaded directly to desktop
Jim Procter [Mon, 7 May 2018 17:08:11 +0000 (18:08 +0100)]
JAL-2321 ensure default is ‘parseImmediately=true’
Jim Procter [Mon, 7 May 2018 16:43:56 +0000 (17:43 +0100)]
JAL-2321 use configured values for structure derived annotation
Jim Procter [Mon, 7 May 2018 16:39:17 +0000 (17:39 +0100)]
JAL-2321 add secondary structure & temp factor if not already present on mapped sequences
Jim Procter [Mon, 7 May 2018 16:38:29 +0000 (17:38 +0100)]
JAL-2321 use StructureImportSettings singleton settings when JmolParser.parse() called from constructor
Jim Procter [Mon, 7 May 2018 16:36:28 +0000 (17:36 +0100)]
JAL-2321 isParseImmediately() allows the parse() method to determine if it was called by the constructor or after construction
Jim Procter [Mon, 7 May 2018 16:35:18 +0000 (17:35 +0100)]
JAL-2321 allow JmolParser to be configured before parsing data
gmungoc [Mon, 7 May 2018 14:16:42 +0000 (15:16 +0100)]
JAL-2808 ensure test setUp/tearDown alwaysRun
gmungoc [Mon, 7 May 2018 13:59:27 +0000 (14:59 +0100)]
Merge branch 'releases/Release_2_10_4_Branch' into develop
Conflicts:
.classpath
Jim Procter [Mon, 7 May 2018 13:23:05 +0000 (14:23 +0100)]
JAL-2906 apply GPLv3 license source
Jim Procter [Mon, 7 May 2018 08:53:05 +0000 (09:53 +0100)]
JAL-2960 don’t override a swing method and create infinite recursion ;) toFront now raiseViewer !
Jim Procter [Mon, 7 May 2018 08:29:54 +0000 (09:29 +0100)]
Merge branch 'releases/Release_2_10_4_Branch' of source.jalview.org/git/jalview into releases/Release_2_10_4_Branch
gmungoc [Fri, 4 May 2018 15:35:02 +0000 (16:35 +0100)]
JAL-2906 small tweaks to release notes
Jim Procter [Fri, 4 May 2018 14:24:49 +0000 (15:24 +0100)]
JAL-2906 2.10.4 release for 8th May 2018
Jim Procter [Fri, 4 May 2018 14:15:16 +0000 (15:15 +0100)]
Merge branch 'bug/JAL-2899' into releases/Release_2_10_4_Branch
Jim Procter [Fri, 4 May 2018 14:05:41 +0000 (15:05 +0100)]
JAL-2906 removed mention of experimental features, updated what’s new for 2.10.4 release, and help TOC.
Jim Procter [Fri, 4 May 2018 13:37:59 +0000 (14:37 +0100)]
JAL-2976 patch NPE when trying to open Uniprot FTS
Jim Procter [Fri, 4 May 2018 13:15:45 +0000 (14:15 +0100)]
JAL-2929 JAL-2922 release notes
Jim Procter [Fri, 4 May 2018 12:55:06 +0000 (13:55 +0100)]
JAL-2976 typo in installAnywhere build for VAqua dependency
Jim Procter [Fri, 4 May 2018 12:26:37 +0000 (13:26 +0100)]
JAL-2960 release notes
Jim Procter [Fri, 4 May 2018 12:26:20 +0000 (13:26 +0100)]
JAL-2948 transfer features/annotation is now available for all users
Jim Procter [Fri, 4 May 2018 12:11:48 +0000 (13:11 +0100)]
JAL-2960 raise the structure view after adding structures to it
Jim Procter [Fri, 4 May 2018 09:35:33 +0000 (10:35 +0100)]
JAL-2976 Vaqua fallback release notes JAL-2906
Jim Procter [Fri, 4 May 2018 07:41:23 +0000 (08:41 +0100)]
Merge branch 'patch/JAL-2976_vaqua4_fallback' into releases/Release_2_10_4_Branch
Jim Procter [Wed, 2 May 2018 14:41:51 +0000 (15:41 +0100)]
JAL-2976 fallback to Vaqua for Macs that don’t work for Quaqua
Jim Procter [Wed, 2 May 2018 14:41:15 +0000 (15:41 +0100)]
JAL-2976 Vaqua(4) as a dependency
Jim Procter [Tue, 1 May 2018 15:59:48 +0000 (16:59 +0100)]
JAL-2899 release notes
Jim Procter [Tue, 1 May 2018 11:31:15 +0000 (12:31 +0100)]
JAL-2973 JAL-2974 known defects for 2.10.4 (JAL-2906)
Jim Procter [Tue, 1 May 2018 11:30:48 +0000 (12:30 +0100)]
JAL-2925 release notes
Jim Procter [Tue, 1 May 2018 10:58:40 +0000 (11:58 +0100)]
JAL-2593 JAL-2945 JAL-2952 JAL-2954 release notes for 2.10.4 JAL-2906
Jim Procter [Tue, 1 May 2018 10:15:50 +0000 (11:15 +0100)]
JAL-2223 JAL-2781 JAL-2780 JAL-2946 JAL-2906 release notes
Jim Procter [Tue, 1 May 2018 09:30:03 +0000 (10:30 +0100)]
JAL-2906 reformat release notes
Jim Procter [Tue, 1 May 2018 09:29:46 +0000 (10:29 +0100)]
JAL-2906 typo
Jim Procter [Tue, 1 May 2018 09:29:19 +0000 (10:29 +0100)]
JAL-2944 revised docs and structure chooser screen shots
Jim Procter [Tue, 1 May 2018 08:21:39 +0000 (09:21 +0100)]
JAL-2899 colouring moved from SwingWorker to a background thread
Jim Procter [Mon, 30 Apr 2018 15:49:41 +0000 (16:49 +0100)]
Merge branch 'bug/JAL-2899' into releases/Release_2_10_4_Branch
Jim Procter [Mon, 30 Apr 2018 09:50:14 +0000 (10:50 +0100)]
JAL-2906 release 2.10.4 on 1st May 2018
Jim Procter [Wed, 25 Apr 2018 11:03:17 +0000 (12:03 +0100)]
Merge branch 'features/JAL-2944_openStructuresInSelectedView' into releases/Release_2_10_4_Branch
gmungoc [Tue, 24 Apr 2018 14:27:36 +0000 (15:27 +0100)]
JAL-2959 no Print dialog shown if Page Format is Cancelled
gmungoc [Tue, 24 Apr 2018 14:08:26 +0000 (15:08 +0100)]
JAL-2939 exit calc thread if no HMM in alignment
gmungoc [Tue, 24 Apr 2018 14:07:25 +0000 (15:07 +0100)]
JAL-591 use constant for Preferences key
gmungoc [Tue, 24 Apr 2018 14:06:05 +0000 (15:06 +0100)]
JAL-2616 unused field removed
gmungoc [Tue, 24 Apr 2018 07:06:03 +0000 (08:06 +0100)]
JAL-2956 unit test
gmungoc [Mon, 23 Apr 2018 14:59:47 +0000 (15:59 +0100)]
JAL-2956 save/restore HMMER profile to/from Jalview project
gmungoc [Mon, 23 Apr 2018 11:27:51 +0000 (12:27 +0100)]
JAL-2954 more efficient SearchResults.markColumns
gmungoc [Mon, 23 Apr 2018 10:26:58 +0000 (11:26 +0100)]
JAL-2952 set negative TempFactor values as AlignmentAnnotation.graphMin
gmungoc [Mon, 23 Apr 2018 08:43:16 +0000 (09:43 +0100)]
JAL-2957 don't validate input on arrow keys
gmungoc [Mon, 23 Apr 2018 08:41:59 +0000 (09:41 +0100)]
JAL-591 ensure slider hidden if text input field only
gmungoc [Fri, 20 Apr 2018 20:59:16 +0000 (21:59 +0100)]
JAL-591 slider scale factor now derived from min-max range
gmungoc [Fri, 20 Apr 2018 17:04:53 +0000 (18:04 +0100)]
JAL-591 tidy and comment code
gmungoc [Fri, 20 Apr 2018 09:05:30 +0000 (10:05 +0100)]
JAL-2629 tweaks to text
gmungoc [Fri, 20 Apr 2018 09:05:08 +0000 (10:05 +0100)]
JAL-591 OptionBox FlowLayout, tweaks to wrapping of options and params
gmungoc [Thu, 19 Apr 2018 15:32:01 +0000 (16:32 +0100)]
JAL-591 utility method renamed and slightly generalised
gmungoc [Wed, 18 Apr 2018 13:22:41 +0000 (14:22 +0100)]
Merge branch 'develop' into features/mchmmer
Conflicts:
.classpath
gmungoc [Wed, 18 Apr 2018 11:41:08 +0000 (12:41 +0100)]
Merge branch 'releases/Release_2_10_4_Branch' into develop
Conflicts:
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
test/jalview/renderer/seqfeatures/FeatureRendererTest.java
gmungoc [Wed, 18 Apr 2018 11:28:37 +0000 (12:28 +0100)]
JAL-2593 render 'duplicate' features if transparency is applied
gmungoc [Wed, 18 Apr 2018 11:13:23 +0000 (12:13 +0100)]
JAL-2629 corrected cutoff parameter passing to hmmsearch
gmungoc [Tue, 17 Apr 2018 17:44:41 +0000 (18:44 +0100)]
Merge branch 'features/mchmmer' of https://source.jalview.org/git/jalview.git into features/mchmmer
Conflicts:
src/jalview/hmmer/HmmerCommand.java
gmungoc [Tue, 17 Apr 2018 17:38:54 +0000 (18:38 +0100)]
JAL-2629 choice of hmm profile now a parameter not a selection, apis simplified
Mungo Carstairs [Tue, 17 Apr 2018 15:01:30 +0000 (16:01 +0100)]
JAL-2937 working Cygwin bash execution of hmmbuild on Windows
gmungoc [Mon, 16 Apr 2018 09:19:31 +0000 (10:19 +0100)]
JAL-2629 JAL-2937 remove redundant is/setHMMConsensusSequence
gmungoc [Mon, 16 Apr 2018 09:18:09 +0000 (10:18 +0100)]
JAL-2937 use preferences for presets, simplify some constructors
gmungoc [Fri, 13 Apr 2018 07:21:00 +0000 (08:21 +0100)]
Merge branch 'features/JAL-2944_openStructuresInSelectedView' of https://source.jalview.org/git/jalview.git into features/JAL-2944_openStructuresInSelectedView
gmungoc [Thu, 12 Apr 2018 15:28:41 +0000 (16:28 +0100)]
JAL-2223 don't add duplicate mappings to StructureSelectionManager
gmungoc [Thu, 12 Apr 2018 13:28:25 +0000 (14:28 +0100)]
JAL-1847 minor post-review updates
gmungoc [Thu, 12 Apr 2018 13:01:26 +0000 (14:01 +0100)]
JAL-2944 tidies for review comments
Jim Procter [Wed, 11 Apr 2018 15:42:02 +0000 (16:42 +0100)]
JAL-2946 catch unexpected SIFTS mapping exceptions and failover to Needleman and Wunsch mapping
Mungo Carstairs [Mon, 9 Apr 2018 16:09:32 +0000 (17:09 +0100)]
JAL-2937 Cygwin path preference, method refactoring
Mungo Carstairs [Mon, 9 Apr 2018 16:07:09 +0000 (17:07 +0100)]
JAL-2629 more error checking
Mungo Carstairs [Mon, 9 Apr 2018 16:04:42 +0000 (17:04 +0100)]
JAL-2937 extract reusable utility method
Mungo Carstairs [Mon, 9 Apr 2018 16:03:40 +0000 (17:03 +0100)]
JAL-2069 typo
git://source.jalview.org / jalview.git / log