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JAL-4366 hacked in a 1:1 mapping
[jalview.git]
/
src
/
jalview
/
bin
/
2023-03-28
Ben Soares
JAL-629 Opening files in new windows. not working yet
tree
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commitdiff
2023-03-25
Ben Soares
JAL-629 open initial non-Arg arguments as files in...
tree
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commitdiff
2023-03-25
Ben Soares
JAL-629 improvements to argparser toString. Improvement...
tree
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commitdiff
2023-03-24
Ben Soares
JAL-629 Test tidyup
tree
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commitdiff
2023-03-23
Ben Soares
JAL-629 refactor ArgParser and helper classes all to...
tree
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commitdiff
2023-03-18
Ben Soares
JAL-629 Check for new commandsSuccess before quit
tree
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commitdiff
2023-03-18
Ben Soares
JAL-629 move getdown update to earlier stage
tree
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commitdiff
2023-03-17
Ben Soares
JAL-629 All applications System.exits going through...
tree
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commitdiff
2023-03-16
Ben Soares
JAL-629 revert metal laf
tree
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commitdiff
2023-03-16
Ben Soares
JAL-629 Set Metal as default LAF for build server tests
tree
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commitdiff
2023-03-15
Ben Soares
JAL-629 Commands more objecty, less classy. FileLoader...
tree
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commitdiff
2023-03-12
Ben Soares
JAL-629 Allow substitutions of {} = defaultCounter...
tree
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commitdiff
2023-03-11
Ben Soares
JAL-629 --substitutions --nosubstitutions flags, -...
tree
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commitdiff
2023-03-11
Ben Soares
JAL-629 Auto and Default count incrementer args. Flags...
tree
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commitdiff
2023-03-10
Ben Soares
JAL-629 start of tests and more examples
tree
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commitdiff
2023-03-09
Ben Soares
JAL-629 start of tests
tree
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commitdiff
2023-03-09
Ben Soares
JAL-629 --argfile=glob implemented. Remove reference...
tree
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commitdiff
2023-03-08
Ben Soares
JAL-629 --close individually for each AlignFrame opened...
tree
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commitdiff
2023-03-08
Ben Soares
JAL-629 --quiet [no stdout], --quiet --quiet [no stderr...
tree
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commitdiff
2023-03-08
Ben Soares
JAL-629 Fix --headless for new args. Fix progressbar...
tree
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commitdiff
2023-03-03
Ben Soares
JAL-629 Improved consistency of ArgParser classes ...
tree
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commitdiff
2023-03-02
Ben Soares
JAL-629 Some refactoring to allow more flexible use...
tree
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commitdiff
2023-02-28
Ben Soares
JAL-629 Firm up bootstrapArgs. Correct '-colour' in...
tree
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commitdiff
2023-02-27
Ben Soares
JAL-629 Fix Exceptions when running with CLI not headless
tree
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commitdiff
2023-02-27
Ben Soares
JAL-629 removed debug prints. added .cif. added some...
tree
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commitdiff
2023-02-24
Ben Soares
Merge branch 'develop' into features/r2_11_2_alphafold...
tree
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commitdiff
2023-02-24
James Procter
Merge branch 'features/r2_11_2_alphafold/JAL-629' into...
features/JAL-3858_PAEsInProjects
tree
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commitdiff
2023-02-24
Ben Soares
JAL-629 helper function for getting sensible structure...
tree
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commitdiff
2023-02-24
Ben Soares
JAL-629 Made ArgValuesMap helper class, simplifies...
tree
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commitdiff
2023-02-23
Ben Soares
JAL-629 bootstrap args and properties. Remember index...
tree
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commitdiff
2023-02-22
Ben Soares
Merge branch 'develop' into features/r2_11_2_alphafold...
tree
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commitdiff
2023-02-20
Ben Soares
JAL-3416 Turn off (partial) flatlaf scaling for HiDPI...
tree
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commitdiff
2023-02-16
James Procter
Merge branch 'features/r2_11_2_alphafold/JAL-629' into...
tree
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commitdiff
2023-02-03
Ben Soares
JAL-629 Fasta sequence id reading whitespace fix. Flexi...
tree
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commitdiff
2023-01-30
Ben Soares
JAL-1988 Make sensible choices if only the opening...
merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
tree
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commitdiff
2023-01-26
Ben Soares
JAL-629 adjust arg type for tempfac-shading -- was...
tree
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commitdiff
2023-01-24
James Procter
JAL-629 hacked in --tempfac-shading - hardcoded to...
tree
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commitdiff
2023-01-24
James Procter
JAL-629 suggest not breaking out of the structure proce...
tree
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commitdiff
2023-01-24
James Procter
JAL-629 don’t carry on Jalview.main if we’ve already...
tree
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commitdiff
2023-01-24
James Procter
JAL-629 don’t trash user’s system property file when...
tree
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commitdiff
2023-01-24
James Procter
JAL-629 don’t complain for Unary args
tree
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commitdiff
2023-01-24
James Procter
JAL-629 labelled breaks are frowned upon by everyone
tree
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commitdiff
2023-01-23
Ben Soares
JAL-629 Attempts to add PAE to structure. --headless...
tree
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commitdiff
2023-01-18
Ben Soares
JAL-629 make sequence id key 'seqid'
tree
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commitdiff
2023-01-16
Ben Soares
JAL-3416 More tweaking of FlatLaf. Problem with macOS...
tree
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commitdiff
2023-01-11
Ben Soares
JAL-1988 JAL-3772 Mark the _default_ STARTUP_FILE as...
tree
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commitdiff
2023-01-11
Ben Soares
JAL-629 refactoring TFType. Remove i18n identification...
tree
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commitdiff
2023-01-06
Ben Soares
JAL-3416 More explicit setting of FlatLaf macOS theme
tree
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commitdiff
2023-01-06
Ben Soares
JAL-3416 Upgraded FlatLaf to 3.0 and added macOS theme...
tree
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commitdiff
2022-12-19
Ben Soares
JAL-629 Add image output and quit
tree
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commitdiff
2022-12-15
Ben Soares
JAL-629 move SubId to more logical place. Attempt remov...
tree
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commitdiff
2022-12-14
Ben Soares
JAL-629 Open Structure Viewer from cmdline
tree
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commitdiff
2022-12-09
Ben Soares
JAL-629 null check, fixed tests!
tree
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commitdiff
2022-12-08
Ben Soares
JAL-629 stray code deleted
tree
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commitdiff
2022-12-08
Ben Soares
JAL-629 Allow attachment of pAE file to a particular...
tree
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commitdiff
2022-12-05
Ben Soares
JAL-629 implementation of --tempfac options
tree
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commitdiff
2022-11-23
Ben Soares
JAL-629 Doing things with the command line arguments
tree
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commitdiff
2022-11-16
Ben Soares
Merge branch 'improvement/JAL-3416_default_to_LIVE_DRAG...
tree
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commitdiff
2022-11-16
Ben Soares
JAL-3416 make flatlaf default for linux
improvement/JAL-3416_default_to_LIVE_DRAG_MODE_for_flatlaf
tree
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commitdiff
2022-11-04
Ben Soares
JAL-1998 JAL-3772 JAL-3416 Merge conflict resolution...
tree
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commitdiff
2022-11-02
Ben Soares
JAL-1988 JAL-3772 Moving packages to somewhere more...
tree
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commitdiff
2022-11-01
Ben Soares
JAL-3416 set flatlaf default drag mode to LIVE_DRAG_MODE
tree
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commitdiff
2022-10-27
Ben Soares
Merge branch 'develop' into bug/JAL-1988_JAL-3772_impro...
tree
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commitdiff
2022-10-25
Ben Soares
JAL-3416 Making FlatLaF default for macs due to a probl...
tree
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commitdiff
2022-10-24
Ben Soares
JAL-1988 JAL-3772 Non-blocking modal dialogs for unsave...
tree
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commitdiff
2022-09-23
Ben Soares
JAL-1988 JAL-3772 Quit confirmation dialog boxes with...
tree
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commitdiff
2022-09-23
Ben Soares
JAL-3676 extra information about jalview_properties...
tree
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commitdiff
2022-08-08
Jim Procter
Merge branch 'task/JAL-3991_check_actual_JAVA_VERSION_a...
tree
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commitdiff
2022-06-13
Jim Procter
Merge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS...
tree
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commitdiff
2022-06-13
Ben Soares
JAL-3416 remove flat as default for linux
tree
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commitdiff
2022-06-13
Ben Soares
JAL-3416 Added some mac specific FlatLAF settings....
tree
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commitdiff
2022-04-06
Ben Soares
JAL-3991 JAVA_COMPILE_VERSION put into build_properties...
tree
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commitdiff
2022-03-18
Ben Soares
JAL-3978 Using getdowninstanceappdir and getdowninstanc...
tree
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commitdiff
2022-03-18
Ben Soares
JAL-3978 New tasks to build archive 'old' dir with...
tree
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commitdiff
2022-03-08
Jim Procter
JAL-3746 apply copyright to source
tree
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commitdiff
2022-03-08
Jim Procter
JAL-3438 spotless for 2.11.2.0
tree
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commitdiff
2022-03-08
Ben Soares
JAL-3103 Removed code and unused widgets for defaultBrowser
tree
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commitdiff
2022-03-08
Ben Soares
JAL-3103 Remove BrowserLauncher2 and use Desktop.browse...
tree
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commitdiff
2022-03-07
Ben Soares
JAL-3103 Switched to (a wrapper around) BrowserLauncher2
tree
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commitdiff
2022-03-04
Jim Procter
JAL-3746 JAL-3811 document SHOW_JWS2_SERVICES user...
tree
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commitdiff
2022-03-04
Jim Procter
JAL-3746 JAL-3812 new argument ‘-nohtmltemplates’ and...
tree
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commitdiff
2022-03-04
Jim Procter
JAL-3746 JAL-3813 NOIDENTIFIERSSERVICE preference disab...
tree
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commitdiff
2022-03-04
Jim Procter
JAL-3746 JAL-3814 NONEWS property
tree
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commitdiff
2022-03-02
Jim Procter
Merge branch 'benreview/JAL-3691_for_2_11_2_getdownrebu...
tree
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commitdiff
2022-02-17
Jim Procter
JAL-3959 add key retrieval urls that support CORS neede...
tree
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commitdiff
2022-02-17
Jim Procter
JAL-3691 patch toUpper/toLower to use Locale.ROOT for...
tree
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commitdiff
2022-02-11
Jim Procter
JAL-3949 - refactor logging from jalview.bin.Cache...
tree
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commitdiff
2022-02-11
Ben Soares
JAL-3949 read ~/.jalview_properties before initialising...
tree
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commitdiff
2022-02-11
Ben Soares
JAL-3949 Complete new abstracted logging framework...
tree
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commitdiff
2022-02-04
Ben Soares
JAL-3949 An attempt at converting to Log4j 2 -- no...
tree
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commitdiff
2022-01-28
Ben Soares
Merge branch 'develop' into JAL-3416_different_look_and...
tree
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commitdiff
2022-01-27
Jim Procter
Merge branch 'bug/JAL-3633_read_proxy_settings_from_jal...
tree
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commitdiff
2022-01-10
Ben Soares
JAL-3937 enable AIA download of intermediate certificat...
tree
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commitdiff
2022-01-10
Ben Soares
JAL-3937 enable AIA download of intermediate certificat...
tree
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commitdiff
2021-12-15
Jim Procter
JAL-3933 remove obsolete Castor logging configuration
tree
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commitdiff
2021-12-15
Jim Procter
JAL-3933 configure root logger console appender to...
tree
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commitdiff
2021-12-15
Jim Procter
JAL-3933 remove obsolete Castor logging configuration
tree
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commitdiff
2021-12-15
Jim Procter
JAL-3933 configure root logger console appender to...
tree
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commitdiff
2021-12-14
Ben Soares
JAL-3933 updated log4j and slf4j jars with log4j1.2...
tree
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commitdiff
2021-12-14
Ben Soares
JAL-3933 Updated log4j jars with log4j-2.16.0 and compa...
tree
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commitdiff
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