jalview.git
6 years agoMerge branch 'testpaches/JAL-2719_JAL-1264_testfails' into tasks/JAL-3070_wsinterfaces
Jim Procter [Thu, 2 Aug 2018 10:53:27 +0000 (11:53 +0100)]
Merge branch 'testpaches/JAL-2719_JAL-1264_testfails' into tasks/JAL-3070_wsinterfaces

6 years agoJAL-2719 JAL-1264 add annotation elements so “Add Reference Annotation” menu should... testpaches/JAL-2719_JAL-1264_testfails
Jim Procter [Thu, 2 Aug 2018 10:48:54 +0000 (11:48 +0100)]
JAL-2719 JAL-1264 add annotation elements so “Add Reference Annotation” menu should be shown for the dataset annotation

6 years agoJAL-2994 put ‘\’ first in character class clause of regex - otherwise doesn’t compile...
Jim Procter [Thu, 2 Aug 2018 10:16:20 +0000 (11:16 +0100)]
JAL-2994 put ‘\’ first in character class clause of regex - otherwise doesn’t compile with error ‘Unterminated character class’

6 years agoJAL-3070 clearer test failed error message for REST service tests
Jim Procter [Thu, 2 Aug 2018 10:09:14 +0000 (11:09 +0100)]
JAL-3070 clearer test failed error message for REST service tests

6 years agoJAL-3070 set host URL correctly from parsed description in web service UIinfo
Jim Procter [Thu, 2 Aug 2018 10:07:59 +0000 (11:07 +0100)]
JAL-3070 set host URL correctly from parsed description in web service UIinfo

6 years agoJAL-3070 refactored Client specific code from jalview.ws.jws2.MSA* as implementors...
Jim Procter [Wed, 1 Aug 2018 20:17:29 +0000 (21:17 +0100)]
JAL-3070 refactored Client specific code from jalview.ws.jws2.MSA* as implementors of jalview.ws.api.* interfaces

6 years agoJAL-3070 pull up sequence anonymisation hash, presets and params list.
Jim Procter [Fri, 27 Jul 2018 11:08:13 +0000 (12:08 +0100)]
JAL-3070 pull up sequence anonymisation hash, presets and params list.

6 years agoJAL-3070 pull up logic for offering a parameters dialog for a service to base client...
Jim Procter [Thu, 26 Jul 2018 16:07:08 +0000 (17:07 +0100)]
JAL-3070 pull up logic for offering a parameters dialog for a service to base client class

6 years agoJAL-3070 abstract class for services with adjustable parameters
Jim Procter [Thu, 26 Jul 2018 16:06:12 +0000 (17:06 +0100)]
JAL-3070 abstract class for services with adjustable parameters

6 years agoJAL-3070 use ArgumentI in all public constructors, convert to service specific argume...
Jim Procter [Thu, 26 Jul 2018 13:36:40 +0000 (14:36 +0100)]
JAL-3070 use ArgumentI in all public constructors, convert to service specific argument object only when needed

6 years agoJAL-3070 pull up setWebService and alignFrame reference
Jim Procter [Thu, 26 Jul 2018 12:37:39 +0000 (13:37 +0100)]
JAL-3070 pull up setWebService and alignFrame reference

6 years agoJAL-3070 UIinfo provides JobParameterStoreI
Jim Procter [Thu, 26 Jul 2018 12:12:48 +0000 (13:12 +0100)]
JAL-3070 UIinfo provides JobParameterStoreI

6 years agoJAL-3070 pushed down JABAWS specific args for WsJobParameters to Jws2Client
Jim Procter [Mon, 23 Jul 2018 10:28:58 +0000 (11:28 +0100)]
JAL-3070 pushed down JABAWS specific args for WsJobParameters to Jws2Client

6 years agoJAL-3070 refactored JABAWS specific jalview.gui.WsJobParameters main method - this...
Jim Procter [Mon, 23 Jul 2018 10:27:29 +0000 (11:27 +0100)]
JAL-3070 refactored JABAWS specific jalview.gui.WsJobParameters main method - this looks to be a duplicate of Jws2ParamView which is already marked as an interactive test so needs review

6 years ago final merge for merge/wsinterfaces_mchmmer_JAL-3070_JAL-1950
Jim Procter [Mon, 23 Jul 2018 09:34:18 +0000 (10:34 +0100)]
 final merge for merge/wsinterfaces_mchmmer_JAL-3070_JAL-1950
 Changes to be committed:
modified:   src/jalview/gui/WsJobParameters.java

6 years agoMerge branch 'features/mchmmer' into merge/wsinterfaces_mchmmer_JAL-3070_JAL-1950
Jim Procter [Mon, 23 Jul 2018 07:56:57 +0000 (08:56 +0100)]
Merge branch 'features/mchmmer' into merge/wsinterfaces_mchmmer_JAL-3070_JAL-1950
merging refactored wsui with mchmmer to get latest service parameters goodness.

6 years agoJAL-3070 pull up hostURL and postURL to UIinfo and getter for action ext
Jim Procter [Fri, 20 Jul 2018 15:12:51 +0000 (16:12 +0100)]
JAL-3070 pull up hostURL and postURL to UIinfo and getter for action ext

6 years agoJAL-3070 core service descriptors for JABAWS services abstracted to jalview.ws.api...
Jim Procter [Fri, 20 Jul 2018 13:27:50 +0000 (14:27 +0100)]
JAL-3070 core service descriptors for JABAWS services abstracted to jalview.ws.api.UIinfo
Note: The jws2.WSClient’s ’serviceType’ is now UIinfo.getName() - reflecting that serviceType was actually the name of the service

6 years agoJAL-3070 refactored base analysis action descriptor from RestClient for
Jim Procter [Fri, 20 Jul 2018 11:02:58 +0000 (12:02 +0100)]
JAL-3070 refactored base analysis action descriptor from RestClient for
use in all web service clients

6 years agoMerge branch 'develop' of http://source.jalview.org/git/jalview into develop
Jim Procter [Thu, 12 Jul 2018 13:17:13 +0000 (14:17 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop

6 years agoMerge branch 'task/JAL-3047_clovercoverage' into develop
Jim Procter [Mon, 2 Jul 2018 09:24:54 +0000 (10:24 +0100)]
Merge branch 'task/JAL-3047_clovercoverage' into develop

6 years agoJAL-3047 don’t let the makedist task complete if a clover build was performed
Jim Procter [Mon, 2 Jul 2018 09:24:24 +0000 (10:24 +0100)]
JAL-3047 don’t let the makedist task complete if a clover build was performed

6 years agoJAL-3047 ‘cloverclasses’ build directory for instrumented classes (allow incremental...
Jim Procter [Mon, 2 Jul 2018 09:20:17 +0000 (10:20 +0100)]
JAL-3047 ‘cloverclasses’ build directory for instrumented classes (allow incremental compile and avoid releasing instrumented classes in production builds)

6 years agoJAL-3047 enable clover for testng
Jim Procter [Wed, 27 Jun 2018 17:17:29 +0000 (18:17 +0100)]
JAL-3047 enable clover for testng

6 years agoJAL-3047 ignore clover output dir
Jim Procter [Wed, 27 Jun 2018 17:17:13 +0000 (18:17 +0100)]
JAL-3047 ignore clover output dir

6 years agoJAL-3047 ant -Dclover.jar=../path/to/clover/lib/clover.jar to enable clover for testn...
Jim Procter [Wed, 27 Jun 2018 17:02:52 +0000 (18:02 +0100)]
JAL-3047 ant -Dclover.jar=../path/to/clover/lib/clover.jar to enable clover for testng ant task

6 years agoMerge branch 'task/JAL-3042_remove_SimpleDocument_dependency' into develop
Jim Procter [Tue, 26 Jun 2018 17:38:03 +0000 (18:38 +0100)]
Merge branch 'task/JAL-3042_remove_SimpleDocument_dependency' into develop

6 years agoJAL-3042 remove mention of adjustable search box history length from docs
Jim Procter [Tue, 26 Jun 2018 17:37:27 +0000 (18:37 +0100)]
JAL-3042 remove mention of adjustable search box history length from docs

6 years agoJAL-3042 don't allow user to change default history length for an input box
Jim Procter [Tue, 26 Jun 2018 14:37:38 +0000 (15:37 +0100)]
JAL-3042 don't allow user to change default history length for an input box

6 years agoJAL-3035 removed jdas in libs documentation and noted spring modules as candidates...
Jim Procter [Tue, 26 Jun 2018 16:57:44 +0000 (17:57 +0100)]
JAL-3035 removed jdas in libs documentation and noted spring modules as candidates for removal

6 years agoMerge branch 'tasks/JAL-3035_remove_dasobert_dependency' into develop
Jim Procter [Tue, 26 Jun 2018 16:07:02 +0000 (17:07 +0100)]
Merge branch 'tasks/JAL-3035_remove_dasobert_dependency' into develop

6 years agoJAL-3035 documentation in 2.11 release notes (and 2.11 fictional release date)
Jim Procter [Tue, 26 Jun 2018 16:06:40 +0000 (17:06 +0100)]
JAL-3035 documentation in 2.11 release notes (and 2.11 fictional release date)

6 years agoJAL-3035 remove DAS UI documentation
Jim Procter [Tue, 26 Jun 2018 16:06:12 +0000 (17:06 +0100)]
JAL-3035 remove DAS UI documentation

6 years agoMerge branch 'tasks/JAL-3035_remove_dasobert_dependency' into develop
Jim Procter [Tue, 26 Jun 2018 15:40:46 +0000 (16:40 +0100)]
Merge branch 'tasks/JAL-3035_remove_dasobert_dependency' into develop

6 years agoJAL-3035 - jalview-das is no more !
Jim Procter [Tue, 26 Jun 2018 15:16:15 +0000 (16:16 +0100)]
JAL-3035 - jalview-das is no more !
 - jsdas lib removed
 - DAS settings panel deleted (Feature settings pane has no tabs now)
 - all code for wrapping DAS sources and retrieving sequences and features from them is gone
 - test methods/main methods have been de-dasified or removed if their only purpose was to test DAS source discovery
 - fancy sorting code to account for DAS sequence source names has been removed

6 years agoJAL-3035 (unrelated) random XML error in nbbuild.xml
Jim Procter [Tue, 26 Jun 2018 15:09:45 +0000 (16:09 +0100)]
JAL-3035 (unrelated) random XML error in nbbuild.xml

6 years agoJAL-2755 correct Javadoc and error handling
gmungoc [Thu, 7 Jun 2018 14:40:11 +0000 (15:40 +0100)]
JAL-2755 correct Javadoc and error handling

6 years agoJAL-3013 resolve symlink to hmmer binaries folder features/mchmmer
gmungoc [Wed, 6 Jun 2018 14:33:26 +0000 (15:33 +0100)]
JAL-3013 resolve symlink to hmmer binaries folder

6 years agoMerge branch 'develop' into features/mchmmer
gmungoc [Wed, 6 Jun 2018 14:19:39 +0000 (15:19 +0100)]
Merge branch 'develop' into features/mchmmer

6 years agoJAL-3013 ensure Chimera as a symlink gets resolved
gmungoc [Wed, 6 Jun 2018 14:16:50 +0000 (15:16 +0100)]
JAL-3013 ensure Chimera as a symlink gets resolved

6 years agoJAL-2956 don't load (non-existent) HMMER jar entry in New View
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

6 years agoJAL-3011 include annotation scores in sequence id tooltip and sequence details report
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

6 years agoMerge branch 'develop' into features/mchmmer
gmungoc [Tue, 5 Jun 2018 07:46:09 +0000 (08:46 +0100)]
Merge branch 'develop' into features/mchmmer

6 years agoJAL-2808 update test for revised treatment of 'mixed type' attribute values
gmungoc [Mon, 4 Jun 2018 19:42:53 +0000 (20:42 +0100)]
JAL-2808 update test for revised treatment of 'mixed type' attribute values

6 years agoJAL-3019 correctly form toRange of 'traversed' MapList
gmungoc [Mon, 4 Jun 2018 19:40:07 +0000 (20:40 +0100)]
JAL-3019 correctly form toRange of 'traversed' MapList

6 years agoJAL-3018 updated REST versions to 6.3
gmungoc [Mon, 4 Jun 2018 14:06:21 +0000 (15:06 +0100)]
JAL-3018 updated REST versions to 6.3

6 years agoJAL-2808 don't capture or report min-max for mixed text/numeric attribute
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

6 years agoJAL-2808 pre-fill numeric inequality filter with min/max range value
gmungoc [Thu, 31 May 2018 10:43:40 +0000 (11:43 +0100)]
JAL-2808 pre-fill numeric inequality filter with min/max range value

6 years agoJAL-2629 suppress 'Add Database' menu option in favour of file chooser argument
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

6 years agoJAL-3005 JAL-2629 file chooser argument for HMM search database
gmungoc [Wed, 30 May 2018 11:16:32 +0000 (12:16 +0100)]
JAL-3005 JAL-2629 file chooser argument for HMM search database

6 years agoJAL-3005 JAL-3008 render file chooser and radio button arguments
gmungoc [Wed, 30 May 2018 11:11:21 +0000 (12:11 +0100)]
JAL-3005 JAL-3008 render file chooser and radio button arguments

6 years agoJAL-3008 new parameter type RadioChoiceParameter
gmungoc [Wed, 30 May 2018 11:10:31 +0000 (12:10 +0100)]
JAL-3008 new parameter type RadioChoiceParameter

6 years agoJAL-3005 new argument type FileParameter for file chooser
gmungoc [Wed, 30 May 2018 11:09:51 +0000 (12:09 +0100)]
JAL-3005 new argument type FileParameter for file chooser

6 years agoJAL-3005 refactor updateRecentlyOpened to enable reuse
gmungoc [Tue, 29 May 2018 16:33:08 +0000 (17:33 +0100)]
JAL-3005 refactor updateRecentlyOpened to enable reuse

6 years agoJAL-2994 utility method to match a list of folder/file patterns
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

6 years agoJAL-2994 restrict search to \Program Files\Chimera*
gmungoc [Mon, 28 May 2018 14:22:54 +0000 (15:22 +0100)]
JAL-2994 restrict search to \Program Files\Chimera*

6 years agoJAL-2994 use pattern matches to search for chimera.exe
gmungoc [Mon, 28 May 2018 10:33:18 +0000 (11:33 +0100)]
JAL-2994 use pattern matches to search for chimera.exe

6 years agoMerge branch 'develop' into features/mchmmer
gmungoc [Mon, 28 May 2018 08:56:14 +0000 (09:56 +0100)]
Merge branch 'develop' into features/mchmmer

Conflicts:
src/jalview/bin/Jalview.java

6 years agoMerge branch 'bug/JAL-797' into develop
gmungoc [Mon, 28 May 2018 08:23:26 +0000 (09:23 +0100)]
Merge branch 'bug/JAL-797' into develop

6 years agoMerge remote-tracking branch 'origin/releases/Release_2_10_4_Branch' 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

6 years agoJAL-2999 release date for 2.10.4b1 set for 27th May 2018
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

6 years agoMerge branch 'documentation/JAL-2999_r2104b1' into releases/Release_2_10_4_Branch
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

6 years agoMerge branch 'bug/JAL-2992panelHeight' 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

6 years agoMerge branch 'bug/JAL-1460_dragndropWindows' 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

6 years agoJAL-2992 simpler heuristic for available height bug/JAL-2992panelHeight
gmungoc [Fri, 25 May 2018 12:49:33 +0000 (13:49 +0100)]
JAL-2992 simpler heuristic for available height

6 years agoMerge branch 'bug/JAL-2991_exporttosvgwrapview' into releases/Release_2_10_4_Branch
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

6 years agoMerge branch 'feature/JAL-2994chimeraPath' 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

6 years agoJAL-1460 clarify release notes - and mention that shortcuts are now handled by Jalview
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

6 years agoJAL-2994 add a few future release points for good measure in Chimera path search... feature/JAL-2994chimeraPath
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

6 years agoJAL-1460 temp variable for clearer conditional and some extra brackets for readabilit... bug/JAL-1460_dragndropWindows
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


6 years agoJAL-1460 javadoc
Jim Procter [Fri, 25 May 2018 09:47:11 +0000 (10:47 +0100)]
JAL-1460 javadoc

6 years agoJAL-2995 tooltip on fields with double-click to browse for file
gmungoc [Fri, 25 May 2018 08:13:35 +0000 (09:13 +0100)]
JAL-2995 tooltip on fields with double-click to browse for file

6 years agoJAL-2994 temporary patch with paths to Chimera for Windows
gmungoc [Fri, 25 May 2018 08:13:00 +0000 (09:13 +0100)]
JAL-2994 temporary patch with paths to Chimera for Windows

6 years agoJAL-2999 issues resolved (or nearly so) for 2.10.4b1
Jim Procter [Thu, 24 May 2018 15:34:34 +0000 (16:34 +0100)]
JAL-2999 issues resolved (or nearly so) for 2.10.4b1

6 years agoJAL-2997 additional tests
gmungoc [Thu, 24 May 2018 14:59:49 +0000 (15:59 +0100)]
JAL-2997 additional tests

6 years agoJAL-1460 tidied up the use of windows link file parser
Jim Procter [Thu, 24 May 2018 13:38:59 +0000 (14:38 +0100)]
JAL-1460 tidied up the use of windows link file parser

6 years agoJAL-1460 more complete drag'n'drop debugging info and bugfixes
Jim Procter [Thu, 24 May 2018 12:52:32 +0000 (13:52 +0100)]
JAL-1460 more complete drag'n'drop debugging info and bugfixes

6 years agoJAL-1460 process .lnk files dragged to Jalview when on Windows using WindowsShortCutH...
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..)


6 years agoJAL-1460 new data flavor for URLs added belt-and-braces URL drop code found in Marina...
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.

6 years agoJAL-2993 AlignFrame listen for keystrokes in OverviewPanel
gmungoc [Wed, 23 May 2018 16:14:17 +0000 (17:14 +0100)]
JAL-2993 AlignFrame listen for keystrokes in OverviewPanel

6 years agoJAL-2997 unit test
gmungoc [Wed, 23 May 2018 15:49:53 +0000 (16:49 +0100)]
JAL-2997 unit test

6 years agofix for JAL-2991 - we could do better :/ bug/JAL-2991_exporttosvgwrapview
Jim Procter [Wed, 23 May 2018 15:19:56 +0000 (16:19 +0100)]
fix for JAL-2991 - we could do better :/

6 years agoJAL-2997 handle tab-delimited trailing column number when parsing
gmungoc [Wed, 23 May 2018 14:33:08 +0000 (15:33 +0100)]
JAL-2997 handle tab-delimited trailing column number when parsing

6 years agoJAL-2999 release notes and version bump for jalview 2.10.4b1
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

6 years agoJAL-2895 replace $$Jalview-Version$$ in help.jhm with build version when indexing...
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

6 years agoJAL-2716 fix to reset choice parameter on Revert
gmungoc [Tue, 22 May 2018 16:06:10 +0000 (17:06 +0100)]
JAL-2716 fix to reset choice parameter on Revert

6 years agoJAL-2716 fix broken checkIfModified behaviour
gmungoc [Tue, 22 May 2018 15:05:03 +0000 (16:05 +0100)]
JAL-2716 fix broken checkIfModified behaviour

6 years agoJAL-2629 method refactor and menu tidying
gmungoc [Tue, 22 May 2018 13:02:34 +0000 (14:02 +0100)]
JAL-2629 method refactor and menu tidying

6 years agoJAL-797 Cmd-W act WHEN_IN_FOCUSED_WINDOW bug/JAL-797
gmungoc [Mon, 21 May 2018 14:31:34 +0000 (15:31 +0100)]
JAL-797 Cmd-W act WHEN_IN_FOCUSED_WINDOW

6 years agoJAL-2719 parse bit score annotation from search results
gmungoc [Tue, 15 May 2018 11:19:02 +0000 (12:19 +0100)]
JAL-2719 parse bit score annotation from search results

6 years agoJAL-1264 exclude score-only from 'Add Reference Annotations'
gmungoc [Tue, 15 May 2018 11:02:12 +0000 (12:02 +0100)]
JAL-1264 exclude score-only from 'Add Reference Annotations'

6 years agoJAL-2629 JAL-2937 respect 'align automatically' option for HMMSearch
gmungoc [Tue, 15 May 2018 09:45:22 +0000 (10:45 +0100)]
JAL-2629 JAL-2937 respect 'align automatically' option for HMMSearch

6 years agoJAL-2989 refactoring to reduce code duplication
gmungoc [Mon, 14 May 2018 13:19:31 +0000 (14:19 +0100)]
JAL-2989 refactoring to reduce code duplication

6 years agoJAL-2711 show short file names in search database combo box
gmungoc [Mon, 14 May 2018 11:17:51 +0000 (12:17 +0100)]
JAL-2711 show short file names in search database combo box

6 years agoJAL-2989 support value display names for Option or Parameters combo boxes
gmungoc [Mon, 14 May 2018 11:17:18 +0000 (12:17 +0100)]
JAL-2989 support value display names for Option or Parameters combo boxes

6 years agoJAL-2711 removed unused and flaky utility method
gmungoc [Mon, 14 May 2018 10:47:12 +0000 (11:47 +0100)]
JAL-2711 removed unused and flaky utility method

6 years agoJAL-2939 check for hmm present when processing groups
gmungoc [Mon, 14 May 2018 08:17:37 +0000 (09:17 +0100)]
JAL-2939 check for hmm present when processing groups

6 years agoJAL-2985 show label instead of checkbox for a required (Jalview) Option
gmungoc [Fri, 11 May 2018 15:34:35 +0000 (16:34 +0100)]
JAL-2985 show label instead of checkbox for a required (Jalview) Option

6 years agoMerge branch 'develop' into features/mchmmer
gmungoc [Fri, 11 May 2018 11:25:16 +0000 (12:25 +0100)]
Merge branch 'develop' into features/mchmmer

6 years agoJAL-2986 corrected findIndex for out of range residue value
gmungoc [Fri, 11 May 2018 11:19:52 +0000 (12:19 +0100)]
JAL-2986 corrected findIndex for out of range residue value