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Adapts PCA points to support rectangular selection
[jalview.git]
/
src
/
jalview
/
bin
/
Jalview.java
2023-06-28
Ben Soares
JAL-4001 Remove analytics for --headless mode
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2023-06-21
Ben Soares
JAL-4001 Rationalise user-agent string into HttpUtils
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2023-06-21
Ben Soares
JAL-4001 Change wording from google to plausible or...
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2023-06-20
Ben Soares
JAL-4001 rename the init method
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2023-06-17
Ben Soares
JAL-4001 Check --nousagestats before doing analytics...
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2023-06-16
Ben Soares
JAL-4001 Add a _geo=1 to query string and JSON. Add...
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2023-06-08
Ben Soares
Merge branch 'develop' into task/JAL-4001_migrate_googl...
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2023-06-08
Ben Soares
JAL-3416 FlatLaf SystemInfo failing in JalviewJS. ...
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2023-06-08
Ben Soares
Merge branch 'develop' into task/JAL-4001_migrate_googl...
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2023-06-07
James Procter
JAL-4195 add exception handling for all image output...
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2023-06-07
James Procter
Merge branch 'patch/JAL-4195_cli_eps_export_npe' into...
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2023-06-07
Ben Soares
Merge branch 'develop' into task/JAL-4001_migrate_googl...
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2023-06-06
James Procter
JAL-629 - remove TODO from jalview.bin.Jalview since...
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2023-06-06
James Procter
JAL-1551 a bit of javadoc for Jalview.testoutput methods
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2023-06-01
Ben Soares
JAL-4001 Changed title+message to MessageManager
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2023-06-01
Ben Soares
JAL-4193 JAL-4194 sessionProperties layer in Cache...
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2023-05-30
Ben Soares
JAL-4121 slight refactoring of method name and added...
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2023-05-27
Ben Soares
JAL-4121 Added a NPE check caught in tests. Added ...
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2023-05-27
Ben Soares
JAL-4121 Store Arg.Opts in bootstrapArgs. Change Opt...
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2023-05-26
Ben Soares
JAL-4125 Fixed non-closing external viewers, also added...
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2023-05-25
Ben Soares
JAL-3416 JAL-3820 FlatLaf default for everyone, includi...
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2023-05-24
Ben Soares
JAL-3416 slightly improved colours for tabber pane...
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2023-05-23
Ben Soares
JAL-629 Added --structureimage code and formatting...
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2023-05-22
Ben Soares
JAL-629 --structureimage with formatting args.
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2023-05-19
Ben Soares
JAL-4187 JAL-629 JAL-3830 Fix ArgParser to check for...
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2023-05-19
Ben Soares
JAL-629 Added Arg.Types and additional --help-type...
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2023-05-18
Ben Soares
JAL-629 fixes to typed args
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2023-05-18
Ben Soares
JAL-629 Added 'Type' to args and argvalues
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2023-05-11
Ben Soares
JAL-629 Fix --tempfac. Hide non-working --notempfac...
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2023-05-11
Ben Soares
JAL-629 Added linkedId to ArgValuesMap for reference...
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2023-05-10
Ben Soares
JAL-629 More docs. Usage statement. Adjust some logging...
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2023-05-04
Ben Soares
JAL-629 More NG arguments: --features, --annotations...
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2023-05-03
Ben Soares
JAL-629 added eps and imagemap. Added --output and...
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2023-04-26
Ben Soares
JAL-629 JAL-4167 Added args to tests. Fixed potential...
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2023-04-24
Ben Soares
JAL-629 Add --nowebdiscovery. Distinguish arg=="open...
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2023-04-22
Ben Soares
JAL-629 Test and fix --annotation --ssannotation args...
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2023-04-19
Ben Soares
JAL-629 Now showing temp fac and secondary structure...
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2023-04-12
Ben Soares
JAL-629 parse SubVals once with ArgValue. Ensure SubVal...
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2023-04-04
Ben Soares
JAL-629 Start of Usage statement
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2023-04-04
Ben Soares
JAL-629 --initsubstitutions as a bootstrap arg, new...
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2023-04-03
Ben Soares
JAL-629 added setprop. More filename based substitution...
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2023-03-29
Ben Soares
JAL-629 Added --opennew --nonews --nosplash. Added...
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2023-03-28
Ben Soares
JAL-629 Opening files in new windows. not working yet
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2023-03-23
Ben Soares
JAL-629 refactor ArgParser and helper classes all to...
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2023-03-18
Ben Soares
JAL-629 Check for new commandsSuccess before quit
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2023-03-18
Ben Soares
JAL-629 move getdown update to earlier stage
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2023-03-17
Ben Soares
JAL-629 All applications System.exits going through...
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2023-03-16
Ben Soares
JAL-629 revert metal laf
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2023-03-16
Ben Soares
JAL-629 Set Metal as default LAF for build server tests
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2023-03-15
Ben Soares
JAL-629 Commands more objecty, less classy. FileLoader...
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2023-03-09
Ben Soares
JAL-629 --argfile=glob implemented. Remove reference...
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2023-03-08
Ben Soares
JAL-629 --quiet [no stdout], --quiet --quiet [no stderr...
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2023-03-08
Ben Soares
JAL-629 Fix --headless for new args. Fix progressbar...
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2023-02-28
Ben Soares
JAL-629 Firm up bootstrapArgs. Correct '-colour' in...
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2023-02-27
Ben Soares
JAL-629 Fix Exceptions when running with CLI not headless
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2023-02-24
James Procter
Merge branch 'features/r2_11_2_alphafold/JAL-629' into...
features/JAL-3858_PAEsInProjects
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2023-02-23
Ben Soares
JAL-629 bootstrap args and properties. Remember index...
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2023-02-22
Ben Soares
Merge branch 'develop' into features/r2_11_2_alphafold...
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2023-02-20
Ben Soares
JAL-3416 Turn off (partial) flatlaf scaling for HiDPI...
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2023-02-16
James Procter
Merge branch 'features/r2_11_2_alphafold/JAL-629' into...
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2023-02-03
Ben Soares
JAL-629 Fasta sequence id reading whitespace fix. Flexi...
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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
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2023-01-24
James Procter
JAL-629 don’t carry on Jalview.main if we’ve already...
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2023-01-23
Ben Soares
JAL-629 Attempts to add PAE to structure. --headless...
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2023-01-16
Ben Soares
JAL-3416 More tweaking of FlatLaf. Problem with macOS...
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2023-01-11
Ben Soares
JAL-1988 JAL-3772 Mark the _default_ STARTUP_FILE as...
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2023-01-06
Ben Soares
JAL-3416 More explicit setting of FlatLaf macOS theme
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2023-01-06
Ben Soares
JAL-3416 Upgraded FlatLaf to 3.0 and added macOS theme...
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2022-11-23
Ben Soares
JAL-629 Doing things with the command line arguments
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2022-11-16
Ben Soares
Merge branch 'improvement/JAL-3416_default_to_LIVE_DRAG...
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2022-11-16
Ben Soares
JAL-3416 make flatlaf default for linux
improvement/JAL-3416_default_to_LIVE_DRAG_MODE_for_flatlaf
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2022-11-04
Ben Soares
JAL-1998 JAL-3772 JAL-3416 Merge conflict resolution...
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2022-11-02
Ben Soares
JAL-1988 JAL-3772 Moving packages to somewhere more...
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2022-11-01
Ben Soares
JAL-3416 set flatlaf default drag mode to LIVE_DRAG_MODE
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2022-10-27
Ben Soares
Merge branch 'develop' into bug/JAL-1988_JAL-3772_impro...
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2022-10-25
Ben Soares
JAL-3416 Making FlatLaF default for macs due to a probl...
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2022-10-24
Ben Soares
JAL-1988 JAL-3772 Non-blocking modal dialogs for unsave...
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2022-09-23
Ben Soares
JAL-1988 JAL-3772 Quit confirmation dialog boxes with...
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2022-08-08
Jim Procter
Merge branch 'task/JAL-3991_check_actual_JAVA_VERSION_a...
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2022-06-13
Jim Procter
Merge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS...
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2022-06-13
Ben Soares
JAL-3416 remove flat as default for linux
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2022-06-13
Ben Soares
JAL-3416 Added some mac specific FlatLAF settings....
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2022-04-06
Ben Soares
JAL-3991 JAVA_COMPILE_VERSION put into build_properties...
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2022-03-08
Ben Soares
JAL-3103 Removed code and unused widgets for defaultBrowser
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2022-03-08
Ben Soares
JAL-3103 Remove BrowserLauncher2 and use Desktop.browse...
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2022-03-07
Ben Soares
JAL-3103 Switched to (a wrapper around) BrowserLauncher2
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2022-03-04
Jim Procter
JAL-3746 JAL-3812 new argument ‘-nohtmltemplates’ and...
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2022-03-04
Jim Procter
JAL-3746 JAL-3814 NONEWS property
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2022-02-17
Jim Procter
JAL-3959 add key retrieval urls that support CORS neede...
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2022-02-11
Jim Procter
JAL-3949 - refactor logging from jalview.bin.Cache...
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2022-02-11
Ben Soares
JAL-3949 read ~/.jalview_properties before initialising...
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2022-02-11
Ben Soares
JAL-3949 Complete new abstracted logging framework...
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2022-01-28
Ben Soares
Merge branch 'develop' into JAL-3416_different_look_and...
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2022-01-10
Ben Soares
JAL-3937 enable AIA download of intermediate certificat...
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2022-01-10
Ben Soares
JAL-3937 enable AIA download of intermediate certificat...
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2021-10-05
Ben Soares
JAL-3416 make flat default laf for linux
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2021-10-04
Ben Soares
JAL-3416 updated FlatLaf to 1.6 and added some tabbed...
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2021-10-04
Ben Soares
Merge branch 'develop' into JAL-3416_different_look_and...
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2021-09-21
Ben Soares
JAL-3691 automatic insertion of Locale.ROOT to toUpperC...
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2021-09-15
Jim Procter
JAL-3741 http to https (and jar to jvp for exampleFile...
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