Merge branch 'patch/JAL-4345_pae_epas1_doubleclick' into develop
[jalview.git] / src / jalview /
2023-08-17 Ben SoaresJAL-3830 JAL-4160 Remove --noheadless as --gui does...
2023-08-16 Ben SoaresMerge branch 'develop' into improvement/JAL-3830_remove...
2023-08-16 Ben SoaresJAL-3820 JAL-4189 Move checks for java executable symli...
2023-08-11 Ben SoaresJAL-629 Much better way of dealing with list of filenam...
2023-08-10 Ben SoaresJAL-629 STDOUT documentation. Opt.STDOUT narrower...
2023-08-10 Ben SoaresJAL-629 Change all stdout and stderr output to use...
2023-08-10 Ben SoaresJAL-629 Method to use for printStackTrace
2023-08-09 Ben SoaresJAL-629 Move more stdout messages to stderr when output...
2023-08-09 Ben SoaresJAL-629 Default to FASTA if no format given for output...
2023-08-09 Ben SoaresJAL-629 Enable output to STDOUT when specifying output...
2023-08-09 Ben SoaresJAL-244 Fix window size narrow adjustment not becoming... feature/JAL-244_Automatically_adjust_left_margin_to_avoid_cropping_annotation_labels
2023-08-08 Ben SoaresJAL-244 Added light grey marks to indicate regions...
2023-08-08 Ben SoaresJAL-244 Fix mismatched vertical positioning of sequence...
2023-08-07 Ben SoaresJAL-244 Avoid working on the Ids Graphics object when...
2023-08-04 Ben SoaresJAL-244 Adjust wrapped alignment widths to always maint...
2023-08-02 Ben SoaresJAL-244 Fix buglet with automatic change in id column...
2023-08-01 Ben SoaresJAL-244 More control of automatic idWidth adjustments...
2023-07-27 Ben SoaresMerge branch 'develop' into feature/JAL-244_Automatical...
2023-07-27 Ben SoaresJAL-244 Allow wrap manual adjustments to be smaller...
2023-07-27 Ben SoaresJAL-244 Allow adjusting Id column width in wrap mode...
2023-07-25 Ben SoaresJAL-244 testing without AlignFrame for --wrap
2023-07-21 Ben SoaresJAL-244 Fixed idWidth labels in headless mode for non...
2023-07-20 Ben SoaresJAL-244 More accurate width calculation, allow increase...
2023-07-20 James ProcterJAL-3855 tree title for PAE matrix tree is PAE Matrix... patch/JAL-3855_fixup_pae
2023-07-20 James ProcterJAL-3855 auto select clusters and fix up colouring...
2023-07-19 Ben SoaresJAL-244 Changes to Annotation labels width now adjusts...
2023-07-18 James Procterexploring making PAE storage in projects more efficient
2023-07-18 James ProcterJAL-3855 PAE matrices are transposed on import from...
2023-07-18 James ProcterJAL-3858 fix off-by-one in matrix visualisation and...
2023-07-18 James ProcterJAL-3858 flip diagonal so matrix visualisation is top...
2023-07-18 James ProcterJAL-3858 annotation .height is bigger than graphHeight...
2023-07-17 James ProcterJAL-4119 TRACE level console message reporting download...
2023-07-12 James ProcterJAL-4223 - test and patch to ensure numbering matches...
2023-07-10 James ProcterMerge branch 'improvement/JAL-3830_remove_dock_icon_in_...
2023-07-07 James ProcterJAL-4217 JAL-629 built in 25s time out waiting for...
2023-07-07 James ProcterMerge branch 'patch/JAL-4119_sifts_ftp_split' into...
2023-07-07 James ProcterJAL-4221 update description when transferring annotatio...
2023-07-07 James ProcterJAL-629 even more console debug for --structureviewer...
2023-07-06 James ProcterJAL-629 liberal defensive coding, comments about refact...
2023-07-06 James ProcterJAL-629 make —structure image work again after threadin...
2023-07-06 James ProcterJAL-4217 catch case when the structure viewer doesn...
2023-07-06 James ProcterJAL-4217 interruptedExceptions should also break any...
2023-07-06 James ProcterJAL-4217 wrap imageExport CLI method's call to imageExp...
2023-07-06 James ProcterJAL-4217 wrap imageExport CLI method's call to imageExp...
2023-07-05 James ProcterMerge branch 'patch/JAL-2292_caseSensitivePAE' into...
2023-07-05 James ProcterMerge branch 'patch/JAL-4213_addref_with_selection...
2023-07-04 James ProcterJAL-4117 JAL-1551 source licensing
2023-06-30 James ProcterJAL-4217 try really hard to shut down and dispose of...
2023-06-30 James ProcterJAL-4216 compute size of annotation using start/end...
2023-06-30 Ben SoaresJAL-4001 Added a random id to User-Agent to ensure... task/JAL-4001_Plausible_API
2023-06-29 Ben SoaresJAL-4214 Linux only: Disable menus when internal modal... bug/JAL-4214_system_freeze_when_opening_file_using_gui_in_linux
2023-06-29 James ProcterJAL-4001 analytics url provided by https://jalview...
2023-06-28 Ben SoaresJAL-4214 Make modal internal frame disappear when main...
2023-06-28 Ben SoaresJAL-4001 change Plausible discovery URL
2023-06-28 Ben SoaresJAL-4001 remove stray --headless mode analytic
2023-06-28 Ben SoaresMerge branch 'task/JAL-4001_Plausible_API' into improve...
2023-06-28 Ben SoaresJAL-3820 add java and java.exe from JAVAHOME to list...
2023-06-28 Ben SoaresJAL-4001 remove headless code from analytics
2023-06-28 Ben SoaresJAL-4001 Remove analytics for --headless mode
2023-06-28 Ben SoaresJAL-4214 Close modal internal frame if JRootPane activi...
2023-06-27 Ben SoaresJAL-3416 Don't forget java bin in the correct java...
2023-06-27 Ben SoaresJAL-4001 Added useful props information
2023-06-26 Ben SoaresMerge branch 'develop' into improvement/JAL-4206_improv... improvement/JAL-4206_improve_JalviewFileChooser_for_flatlaf
2023-06-26 Ben SoaresMerge branch 'develop' into improvement/JAL-3830_remove...
2023-06-22 Ben SoaresMerge branch 'develop' into task/JAL-4001_Plausible_API
2023-06-22 Ben SoaresJAL-4001 Fix default API url
2023-06-22 James ProcterJAL-4213 don’t pass active selection when actioning... patch/JAL-4213_addref_with_selection
2023-06-22 James ProcterJAL-4213 - document the addReferenceAnnotations method...
2023-06-22 Ben SoaresJAL-4001 Added 'installation' property.
2023-06-22 James ProcterJAL-2292 - ensure mapping is built for equal symbols... patch/JAL-2292_caseSensitivePAE
2023-06-22 Ben SoaresJAL-4001 Added lookup to https://jalview.org/config...
2023-06-22 Ben SoaresJAL-4019 corrected to '>' to '>=' for percentage compar... bug/JAL-4125_flatlaf_quithandler_external_structureviewers_not_closed
2023-06-21 James ProcterMerge branch 'patch/JAL-4196_structure_viewer_synchroni... patch/JAL-4196_structure_viewer_synchronising
2023-06-21 Ben SoaresJAL-4001 Rationalise user-agent string into HttpUtils
2023-06-21 Ben SoaresJAL-4001 Change wording from google to plausible or...
2023-06-20 Ben SoaresJAL-4001 rename the init method
2023-06-20 Ben SoaresJAL-4001 Working Plausible analytics
2023-06-20 Ben SoaresJAL-4001 Plausible class
2023-06-20 Ben SoaresJAL-4001 Added a genuine client_id (from gtag). Added... task/JAL-4001_migrate_googleanalytics_to_GA4
2023-06-17 Ben SoaresJAL-4001 Check --nousagestats before doing analytics...
2023-06-16 Ben SoaresJAL-3830 Take account of --gui taking precedence over...
2023-06-16 Ben SoaresJAL-3830 Look for --headless mode and add -Djava.awt...
2023-06-16 Ben SoaresJAL-4001 Add a _geo=1 to query string and JSON. Add...
2023-06-16 Ben SoaresJAL-4001 Remove jgoogleanalytics code and jar
2023-06-16 Ben SoaresJAL-4001 make page_location the same encoding as the...
2023-06-15 Ben SoaresJAL-4001 Changed for Java 8 compatibility
2023-06-15 Ben SoaresJAL-4206 Use All Known Alignment Files as default until...
2023-06-14 Ben SoaresJAL-4026 if relative path in recently opened exists...
2023-06-14 Ben SoaresJAL-4206 unified dimensions
2023-06-14 Ben SoaresJAL-4001 Trying to see extra information in GA dashboard
2023-06-14 Ben SoaresMerge branch 'develop' into task/JAL-4001_migrate_googl...
2023-06-14 Ben SoaresJAL-4206 Added recentlyOpenedCellRenderer to better...
2023-06-13 Ben SoaresJAL-3416 Removed a few more JInternalFrame icons with...
2023-06-09 Ben SoaresJAL-3599 Make jalviewjs dependOn jalviewjsLaunchTest...
2023-06-09 Ben SoaresJAL-3599 Deliberate NPE to see if build plan fails
2023-06-08 Ben SoaresJAL-3599 gradle tasks to test JalviewJS launches in...
2023-06-08 Ben SoaresJAL-4001 Only send defaultParams for application_launch...
2023-06-08 Ben SoaresMerge branch 'develop' into task/JAL-4001_migrate_googl...
2023-06-08 James ProcterMerge branch 'develop' into patch/JAL-4196_structure_vi...
2023-06-08 James ProcterJAL-4196 make very sure we avoid CME by defensively...
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