Jim Procter [Wed, 18 Jul 2018 14:25:48 +0000 (15:25 +0100)]
Merge branch 'features/mchmmer' into features/mchmmer_merge_JAL-1950
gmungoc [Wed, 6 Jun 2018 14:33:26 +0000 (15:33 +0100)]
JAL-3013 resolve symlink to hmmer binaries folder
gmungoc [Wed, 6 Jun 2018 14:19:39 +0000 (15:19 +0100)]
Merge branch 'develop' into features/mchmmer
gmungoc [Wed, 6 Jun 2018 14:16:50 +0000 (15:16 +0100)]
JAL-3013 ensure Chimera as a symlink gets resolved
gmungoc [Wed, 6 Jun 2018 11:03:57 +0000 (12:03 +0100)]
JAL-2956 don't load (non-existent) HMMER jar entry in New View
gmungoc [Tue, 5 Jun 2018 08:34:08 +0000 (09:34 +0100)]
JAL-3011 include annotation scores in sequence id tooltip and sequence details report
gmungoc [Tue, 5 Jun 2018 07:46:09 +0000 (08:46 +0100)]
Merge branch 'develop' into features/mchmmer
gmungoc [Mon, 4 Jun 2018 19:42:53 +0000 (20:42 +0100)]
JAL-2808 update test for revised treatment of 'mixed type' attribute values
gmungoc [Mon, 4 Jun 2018 19:40:07 +0000 (20:40 +0100)]
JAL-3019 correctly form toRange of 'traversed' MapList
gmungoc [Mon, 4 Jun 2018 14:06:21 +0000 (15:06 +0100)]
JAL-3018 updated REST versions to 6.3
Jim Procter [Fri, 1 Jun 2018 14:04:43 +0000 (15:04 +0100)]
JAL-3012 JAL-2937 TODO avoid creating data copies by instrumenting output alignment object
Jim Procter [Fri, 1 Jun 2018 14:00:49 +0000 (15:00 +0100)]
JAL-2937 hmmbuild input data generated via AlignmentView from alignment, not directly from viewport
Jim Procter [Fri, 1 Jun 2018 13:59:48 +0000 (14:59 +0100)]
JAL-1950 JAL-2937 allow individual groups to be rematerialised from an alignment view
Jim Procter [Fri, 1 Jun 2018 13:58:55 +0000 (14:58 +0100)]
JAL-1551 formatting
Jim Procter [Fri, 1 Jun 2018 13:57:08 +0000 (14:57 +0100)]
JAL-1950 JAL-2937 allow copy of group without sequences being also copied to cloned group
Jim Procter [Fri, 1 Jun 2018 13:47:35 +0000 (14:47 +0100)]
JAL-1950 JAL-2937 allow copy of sequences from group without annotations
Jim Procter [Thu, 31 May 2018 16:35:35 +0000 (17:35 +0100)]
JAL-1950 JAL-2629 insert gaps into HMM used to search DB - AVOIDS NEED TO RUN HMMALIGN AFTERWARDS !
Jim Procter [Thu, 31 May 2018 16:34:56 +0000 (17:34 +0100)]
JAL-2629 (probably not right issue) JAL-1950 - make a new alignment sequence version of HMM that was used to search the database before adding to results to avoid breaking jalview’s alignment data model!
Jim Procter [Thu, 31 May 2018 16:30:49 +0000 (17:30 +0100)]
JAL-3011 JAL-2719 JAL-1958 add posterior probability scores to score and value annotation rows, and show reference positions and global posterior probability score on results
Jim Procter [Thu, 31 May 2018 16:27:13 +0000 (17:27 +0100)]
JAL-3011 - show score in annotation row - looks like this got lost in an automerge
Jim Procter [Thu, 31 May 2018 16:20:31 +0000 (17:20 +0100)]
JAL-1958 use the annotation score for the sequence being coloured !
Jim Procter [Thu, 31 May 2018 16:20:00 +0000 (17:20 +0100)]
JAL-1950 JAL-1958 disable per-row score modulation if none present
gmungoc [Thu, 31 May 2018 13:20:50 +0000 (14:20 +0100)]
JAL-2808 don't capture or report min-max for mixed text/numeric attribute
Jim Procter [Thu, 31 May 2018 12:48:14 +0000 (13:48 +0100)]
Merge branch 'spike/JAL-1950_hmmer3client' into features/mchmmer_merge_JAL-1950
Conflicts:
src/jalview/gui/AlignViewport.java
Jim Procter [Thu, 31 May 2018 12:41:36 +0000 (13:41 +0100)]
Merge branch 'develop' into spike/JAL-1950_hmmer3client
gmungoc [Thu, 31 May 2018 10:43:40 +0000 (11:43 +0100)]
JAL-2808 pre-fill numeric inequality filter with min/max range value
gmungoc [Wed, 30 May 2018 11:19:35 +0000 (12:19 +0100)]
JAL-2629 suppress 'Add Database' menu option in favour of file chooser argument
gmungoc [Wed, 30 May 2018 11:16:32 +0000 (12:16 +0100)]
JAL-3005 JAL-2629 file chooser argument for HMM search database
gmungoc [Wed, 30 May 2018 11:11:21 +0000 (12:11 +0100)]
JAL-3005 JAL-3008 render file chooser and radio button arguments
gmungoc [Wed, 30 May 2018 11:10:31 +0000 (12:10 +0100)]
JAL-3008 new parameter type RadioChoiceParameter
gmungoc [Wed, 30 May 2018 11:09:51 +0000 (12:09 +0100)]
JAL-3005 new argument type FileParameter for file chooser
gmungoc [Tue, 29 May 2018 16:33:08 +0000 (17:33 +0100)]
JAL-3005 refactor updateRecentlyOpened to enable reuse
Mungo Carstairs [Tue, 29 May 2018 10:24:00 +0000 (11:24 +0100)]
JAL-2994 utility method to match a list of folder/file patterns
gmungoc [Mon, 28 May 2018 14:22:54 +0000 (15:22 +0100)]
JAL-2994 restrict search to \Program Files\Chimera*
gmungoc [Mon, 28 May 2018 10:33:18 +0000 (11:33 +0100)]
JAL-2994 use pattern matches to search for chimera.exe
gmungoc [Mon, 28 May 2018 08:56:14 +0000 (09:56 +0100)]
Merge branch 'develop' into features/mchmmer
Conflicts:
src/jalview/bin/Jalview.java
gmungoc [Mon, 28 May 2018 08:23:26 +0000 (09:23 +0100)]
Merge branch 'bug/JAL-797' into develop
gmungoc [Mon, 28 May 2018 08:19:40 +0000 (09:19 +0100)]
Merge remote-tracking branch 'origin/releases/Release_2_10_4_Branch' into develop
Conflicts:
src/jalview/io/FeaturesFile.java
Jim Procter [Sat, 26 May 2018 12:36:41 +0000 (13:36 +0100)]
JAL-2999 release date for 2.10.4b1 set for 27th May 2018
Jim Procter [Fri, 25 May 2018 12:58:10 +0000 (13:58 +0100)]
Merge branch 'documentation/JAL-2999_r2104b1' into releases/Release_2_10_4_Branch
Jim Procter [Fri, 25 May 2018 12:58:01 +0000 (13:58 +0100)]
Merge branch 'bug/JAL-2992panelHeight' into releases/Release_2_10_4_Branch
Jim Procter [Fri, 25 May 2018 12:56:34 +0000 (13:56 +0100)]
Merge branch 'bug/JAL-1460_dragndropWindows' into releases/Release_2_10_4_Branch
gmungoc [Fri, 25 May 2018 12:49:33 +0000 (13:49 +0100)]
JAL-2992 simpler heuristic for available height
Jim Procter [Fri, 25 May 2018 10:19:58 +0000 (11:19 +0100)]
Merge branch 'bug/JAL-2991_exporttosvgwrapview' into releases/Release_2_10_4_Branch
Jim Procter [Fri, 25 May 2018 10:10:20 +0000 (11:10 +0100)]
Merge branch 'feature/JAL-2994chimeraPath' into releases/Release_2_10_4_Branch
Jim Procter [Fri, 25 May 2018 10:09:33 +0000 (11:09 +0100)]
JAL-1460 clarify release notes - and mention that shortcuts are now handled by Jalview
Jim Procter [Fri, 25 May 2018 09:59:51 +0000 (10:59 +0100)]
JAL-2994 add a few future release points for good measure in Chimera path search on Windows
Jim Procter [Fri, 25 May 2018 09:47:32 +0000 (10:47 +0100)]
JAL-1460 temp variable for clearer conditional and some extra brackets for readability only
Jim Procter [Fri, 25 May 2018 09:47:11 +0000 (10:47 +0100)]
JAL-1460 javadoc
gmungoc [Fri, 25 May 2018 08:13:35 +0000 (09:13 +0100)]
JAL-2995 tooltip on fields with double-click to browse for file
gmungoc [Fri, 25 May 2018 08:13:00 +0000 (09:13 +0100)]
JAL-2994 temporary patch with paths to Chimera for Windows
Jim Procter [Thu, 24 May 2018 15:34:34 +0000 (16:34 +0100)]
JAL-2999 issues resolved (or nearly so) for 2.10.4b1
gmungoc [Thu, 24 May 2018 14:59:49 +0000 (15:59 +0100)]
JAL-2997 additional tests
Jim Procter [Thu, 24 May 2018 13:38:59 +0000 (14:38 +0100)]
JAL-1460 tidied up the use of windows link file parser
Jim Procter [Thu, 24 May 2018 12:52:32 +0000 (13:52 +0100)]
JAL-1460 more complete drag'n'drop debugging info and bugfixes
Jim Procter [Thu, 24 May 2018 10:56:32 +0000 (11:56 +0100)]
JAL-1460 process .lnk files dragged to Jalview when on Windows using WindowsShortCutHandler class (thanks to StackOverFlow post..)
Jim Procter [Thu, 24 May 2018 10:54:26 +0000 (11:54 +0100)]
JAL-1460 new data flavor for URLs added belt-and-braces URL drop code found in Marinacci and Adamson’s ’Swing Hacks’ (https://books.google.co.uk/books?id=oNbFfcyAtv4C&lpg=PA336&ots=hflsI561Dv&dq=java%20drag%20and%20drop%20url&pg=PA337#v=onepage&q=java%20drag%20and%20drop%20url&f=false ) plus OS X bug workaround.
gmungoc [Wed, 23 May 2018 16:14:17 +0000 (17:14 +0100)]
JAL-2993 AlignFrame listen for keystrokes in OverviewPanel
gmungoc [Wed, 23 May 2018 15:49:53 +0000 (16:49 +0100)]
JAL-2997 unit test
Jim Procter [Wed, 23 May 2018 15:19:56 +0000 (16:19 +0100)]
fix for JAL-2991 - we could do better :/
gmungoc [Wed, 23 May 2018 14:33:08 +0000 (15:33 +0100)]
JAL-2997 handle tab-delimited trailing column number when parsing
Jim Procter [Wed, 23 May 2018 14:18:52 +0000 (15:18 +0100)]
JAL-2999 release notes and version bump for jalview 2.10.4b1
Jim Procter [Wed, 23 May 2018 14:17:45 +0000 (15:17 +0100)]
JAL-2895 replace $$Jalview-Version$$ in help.jhm with build version when indexing built in help pages
gmungoc [Tue, 22 May 2018 16:06:10 +0000 (17:06 +0100)]
JAL-2716 fix to reset choice parameter on Revert
gmungoc [Tue, 22 May 2018 15:05:03 +0000 (16:05 +0100)]
JAL-2716 fix broken checkIfModified behaviour
gmungoc [Tue, 22 May 2018 13:02:34 +0000 (14:02 +0100)]
JAL-2629 method refactor and menu tidying
gmungoc [Mon, 21 May 2018 14:31:34 +0000 (15:31 +0100)]
JAL-797 Cmd-W act WHEN_IN_FOCUSED_WINDOW
gmungoc [Tue, 15 May 2018 11:19:02 +0000 (12:19 +0100)]
JAL-2719 parse bit score annotation from search results
gmungoc [Tue, 15 May 2018 11:02:12 +0000 (12:02 +0100)]
JAL-1264 exclude score-only from 'Add Reference Annotations'
gmungoc [Tue, 15 May 2018 09:45:22 +0000 (10:45 +0100)]
JAL-2629 JAL-2937 respect 'align automatically' option for HMMSearch
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
git://source.jalview.org / jalview.git / log