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[jalview.git] / src / jalview / gui / Preferences.java

2018-02-20	gmungoc	Merge branch 'develop' into features/mchmmer	blob \| commitdiff
2018-02-19	gmungoc	JAL-2629 refactoring of Hmmer preferences	blob \| commitdiff \| diff to current
2018-01-10	gmungoc	JAL-1793 update spike branch to latest	blob \| commitdiff \| diff to current
2017-11-30	Jim Procter	JAL-2849 JAL-2863 file format preferences TODO	blob \| commitdiff \| diff to current
2017-10-03	gmungoc	JAL-2738 copy to spikes/mungo	blob \| commitdiff \| diff to current
2017-09-04	Jim Procter	JAL-2527 move default colours for applet / application...	blob \| commitdiff \| diff to current
2017-09-01	TZVanaalten	JAL-2629 fix hmmbuild validation failing if no AlignFra...	blob \| commitdiff \| diff to current
2017-08-31	kiramt	JAL-2527 Updates following code review	blob \| commitdiff \| diff to current
2017-08-30	kiramt	JAL-2527 Added default setting/resetting and first...	blob \| commitdiff \| diff to current
2017-08-29	kiramt	JAL-2527 Added overview prefs - don't get picked up...	blob \| commitdiff \| diff to current
2017-08-28	kiramt	JAL-2527 Started adding overview preferences	blob \| commitdiff \| diff to current
2017-08-28	TZVanaalten	JAL-2629 fix HMMER validation fail due to checking...	blob \| commitdiff \| diff to current
2017-08-25	TZVanaalten	JAL-2629 add ability to add and select a DB for hmmsearch	blob \| commitdiff \| diff to current
2017-08-18	TZVanaalten	Merge branch 'develop' into features/hmmer	blob \| commitdiff \| diff to current
2017-08-16	Jim Procter	JAL-2418 source formatting	blob \| commitdiff \| diff to current
2017-08-16	TZVanaalten	JAL-2629 add hmmbuild validation check which also gets...	blob \| commitdiff \| diff to current
2017-08-15	TZVanaalten	JAL-2629 add checks for executing hmmer commands as...	blob \| commitdiff \| diff to current
2017-08-15	tzvanaalten	JAL-2629 fix file loading issues on Mac	blob \| commitdiff \| diff to current
2017-08-15	TZVanaalten	JAL-2629 add HMMER version check	blob \| commitdiff \| diff to current
2017-08-15	TZVanaalten	JAL-2629 the HMMER tab is now disabled when HMMER is...	blob \| commitdiff \| diff to current
2017-08-14	TZVanaalten	JAL-2629 add validation for HMMER path	blob \| commitdiff \| diff to current
2017-08-13	TZVanaalten	JAL-2629 add HMMER tab in preferences menu	blob \| commitdiff \| diff to current
2017-08-08	TZVanaalten	JAL-2629 add ability to select hmmer binaries folder	blob \| commitdiff \| diff to current
2017-07-25	TZVanaalten	JAL-2629 add non-functional HMMER menu	blob \| commitdiff \| diff to current
2017-06-09	gmungoc	JAL-2446 merged to spike branch	blob \| commitdiff \| diff to current
2017-04-27	Jim Procter	JAL-1933 desktop preferences for occupancy	blob \| commitdiff \| diff to current
2017-02-08	kiramt	Merge remote-tracking branch 'origin/develop' into...	blob \| commitdiff \| diff to current
2017-01-27	kiramt	JAL-2366 Removed unneeded setEnabled calls	blob \| commitdiff \| diff to current
2017-01-26	kiramt	Merge remote-tracking branch 'origin/develop' into...	blob \| commitdiff \| diff to current
2017-01-17	gmungoc	Merge branch 'develop' into features/JAL-2360colourSche...	blob \| commitdiff \| diff to current
2017-01-11	gmungoc	JAL-2344 FileFormats singleton for formats, FileFormatI...	blob \| commitdiff \| diff to current
2016-12-20	gmungoc	JAL-2360 ColourSchemes holds configured schemes, AlignF...	blob \| commitdiff \| diff to current
2016-12-16	kiramt	JAL-2316 Added database name column to URL links table...	blob \| commitdiff \| diff to current
2016-12-16	gmungoc	JAL-2360 refactoring for JalviewColourScheme enum,	blob \| commitdiff \| diff to current
2016-12-15	kiramt	JAL-2316 Changes following review.	blob \| commitdiff \| diff to current
2016-12-13	kiramt	Merge branch 'develop' into features/JAL-2316	blob \| commitdiff \| diff to current
2016-12-12	kiramt	JAL-2316 Added GUI checks for duplicate link ids	blob \| commitdiff \| diff to current
2016-12-12	kiramt	JAL-2316 Unit test update to UrlLinkTableModel and...	blob \| commitdiff \| diff to current
2016-12-12	kiramt	JAL-2316 Added jalview.urls.* packages	blob \| commitdiff \| diff to current
2016-12-09	kiramt	JAL-2316 Unit test updates and associated minor changes...	blob \| commitdiff \| diff to current
2016-12-07	gmungoc	JAL-2344 handle null format, simplify JalviewFileChoose...	blob \| commitdiff \| diff to current
2016-12-07	kiramt	JAL-2316 Restructure identifiers.org download	blob \| commitdiff \| diff to current
2016-12-05	kiramt	JAL-2316 Added UrlProvider factories. Tidied up labelling.	blob \| commitdiff \| diff to current
2016-12-05	kiramt	JAL-2316 Adjusted unit tests. Tidied UrlLinkProviderI...	blob \| commitdiff \| diff to current
2016-12-02	kiramt	JAL-2316 GUI updates to Connections tab in Preferences...	blob \| commitdiff \| diff to current
2016-11-28	gmungoc	Merge branch 'develop' into trialMerge	blob \| commitdiff \| diff to current
2016-11-25	gmungoc	Merge branch 'develop' into trialMerge	blob \| commitdiff \| diff to current
2016-11-24	tcofoegbu	JAL-2326 updated references of JOptionPane to JvOptionPane	blob \| commitdiff \| diff to current
2016-11-24	gmungoc	Further tweaks to get tests passing	blob \| commitdiff \| diff to current
2016-11-15	kiramt	JAL-2316 Moved url providers into own package	blob \| commitdiff \| diff to current
2016-11-15	kiramt	JAL-2316 Refactoring of functionality to provide urls...	blob \| commitdiff \| diff to current
2016-11-14	kiramt	Url links changes - incomplete checkin as battery low	blob \| commitdiff \| diff to current
2016-11-04	kiramt	JAL-2315 Clear sequenceURLLinks if all sequence links...	blob \| commitdiff \| diff to current
2016-11-02	kiramt	JAL-2282 Renamed internal use of sequence id / db acces...	blob \| commitdiff \| diff to current
2016-10-31	kiramt	Use ACCESSION_ID for database accession id, and SEQUENC...	blob \| commitdiff \| diff to current
2016-10-25	Jim Procter	JAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch	blob \| commitdiff \| diff to current
2016-10-24	kiramt	Correct Preferences to check for SEQUENCE_NAME as well...	blob \| commitdiff \| diff to current
2016-10-22	kiramt	Working links menu	blob \| commitdiff \| diff to current
2016-10-21	kiramt	Factored URL Link constants out into UrlConstants file.	blob \| commitdiff \| diff to current
2016-10-06	Jim Procter	JAL-2089 Merge branch releases/Release_2_10_Branch...	blob \| commitdiff \| diff to current
2016-10-05	Jim Procter	JAL-2189 source formatting	blob \| commitdiff \| diff to current
2016-08-30	gmungoc	Merge branch 'develop' into features/filetypeEnum	blob \| commitdiff \| diff to current
2016-07-12	gmungoc	FileFormat enum wip changes	blob \| commitdiff \| diff to current
2016-07-11	gmungoc	file format enum wip changes	blob \| commitdiff \| diff to current
2016-05-27	gmungoc	JAL-1911 use existing object when setting 'Prompt each...	blob \| commitdiff \| diff to current
2016-05-27	tcofoegbu	JAL-1911 further improvement to bugfix - do not save...	blob \| commitdiff \| diff to current
2016-05-26	tcofoegbu	JAL-1911 improvement to bugfix - do not save i18n text...	blob \| commitdiff \| diff to current
2016-05-26	tcofoegbu	JAL-1911 bugfix - do not save i18n text in preference...	blob \| commitdiff \| diff to current
2016-04-14	gmungoc	JAL-1421 type parameter added to some collections	blob \| commitdiff \| diff to current
2016-04-12	gmungoc	JAL-2050 only hide introns if exons are present! Remove...	blob \| commitdiff \| diff to current
2016-04-11	gmungoc	JAL-1705 (new preference option to) hide introns when...	blob \| commitdiff \| diff to current
2015-11-25	tcofoegbu	JAL-1479 bugfix after decoupling SIFTS preference settings	blob \| commitdiff \| diff to current
2015-11-17	tcofoegbu	JAL-1479 Refactored Sifts configuration preference...	blob \| commitdiff \| diff to current
2015-10-22	tcofoegbu	JAL-1479 implemented preferences for SIFTs / Needleman...	blob \| commitdiff \| diff to current
2015-10-16	Jim Procter	JAL-1925 update source version in license Release_2_9_0b2	blob \| commitdiff \| diff to current
2015-10-08	Jim Procter	JAL-1894 update year/version in copyright	blob \| commitdiff \| diff to current
2015-09-10	Jim Procter	JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...	blob \| commitdiff \| diff to current
2015-09-10	Jim Procter	JAL-1645 source formatting and organise imports	blob \| commitdiff \| diff to current
2015-09-02	gmungoc	JAL-1768 set initial 'enabled' state for id width label...	blob \| commitdiff \| diff to current
2015-09-02	gmungoc	JAL-1768 enable fixed width output when auto-width...	blob \| commitdiff \| diff to current
2015-08-18	tcofoegbu	JAL-1835 added UI for BioJSON embbeding preference	blob \| commitdiff \| diff to current
2015-04-13	gmungoc	JAL-1695 new property ENABLE_SPLIT_FRAME	blob \| commitdiff \| diff to current
2015-04-02	gmungoc	JAL-1690 'scale protein as cDNA' options in Preferences...	blob \| commitdiff \| diff to current
2015-03-26	gmungoc	Merge develop to Release_2_8_3_Branch	blob \| commitdiff \| diff to current
2015-03-06	Jim Procter	JAL-1683 replace year/version strings with tokens in...	blob \| commitdiff \| diff to current
2015-03-06	Jim Procter	Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e...	blob \| commitdiff \| diff to current
2015-01-07	gmungoc	JAL-1588 refactoring to StructureViewerBase and related	blob \| commitdiff \| diff to current
2014-12-22	Jim Procter	Merge: 497958b 68dcaa7	blob \| commitdiff \| diff to current
2014-12-15	Jim Procter	JAL-1620 version bump and release notes	blob \| commitdiff \| diff to current
2014-11-27	gmungoc	JAL-1603 if Chimera selected in Preferences, warn if...	blob \| commitdiff \| diff to current
2014-11-18	gmungoc	Merge branch 'Release_2_8_2_Branch' of https://source...	blob \| commitdiff \| diff to current
2014-11-18	Jim Procter	JAL-674 make temperature factor, local secondary struct...	blob \| commitdiff \| diff to current
2014-11-17	gmungoc	JAL-1586 chimera file chooser added, validate on OK...	blob \| commitdiff \| diff to current
2014-11-17	gmungoc	JAL-1528 new Preference CHIMERA_PATH (Preferences ...	blob \| commitdiff \| diff to current
2014-11-13	gmungoc	JAL-1528 new Preference CHIMERA_PATH (Preferences ...	blob \| commitdiff \| diff to current
2014-11-05	gmungoc	JAL-1152 new Structure tab on Preferences for SS deriva...	blob \| commitdiff \| diff to current
2014-11-03	gmungoc	JAL-1152 annotation sorting preferences and help docume...	blob \| commitdiff \| diff to current
2014-09-23	darolmar	JAL-1355	blob \| commitdiff \| diff to current
2014-09-19	darolmar	JAL-1355	blob \| commitdiff \| diff to current
2014-06-06	Jim Procter	JAL-1517 source formatting	blob \| commitdiff \| diff to current
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