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JAL-4134 JAL-3855 store/restore groups, tree and threshold used to cluster a PAE...
[jalview.git] / src / jalview / bin /
2023-03-08 Ben SoaresJAL-629 Fix --headless for new args. Fix progressbar... tree | commitdiff
2023-03-03 Ben SoaresJAL-629 Improved consistency of ArgParser classes ... tree | commitdiff
2023-03-02 Ben SoaresJAL-629 Some refactoring to allow more flexible use... tree | commitdiff
2023-02-28 Ben SoaresJAL-629 Firm up bootstrapArgs. Correct '-colour' in... tree | commitdiff
2023-02-27 Ben SoaresJAL-629 Fix Exceptions when running with CLI not headless tree | commitdiff
2023-02-27 Ben SoaresJAL-629 removed debug prints. added .cif. added some... tree | commitdiff
2023-02-24 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... tree | commitdiff
2023-02-24 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-629' into... features/JAL-3858_PAEsInProjects tree | commitdiff
2023-02-24 Ben SoaresJAL-629 helper function for getting sensible structure... tree | commitdiff
2023-02-24 Ben SoaresJAL-629 Made ArgValuesMap helper class, simplifies... tree | commitdiff
2023-02-23 Ben SoaresJAL-629 bootstrap args and properties. Remember index... tree | commitdiff
2023-02-22 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... tree | commitdiff
2023-02-20 Ben SoaresJAL-3416 Turn off (partial) flatlaf scaling for HiDPI... tree | commitdiff
2023-02-16 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-629' into... tree | commitdiff
2023-02-03 Ben SoaresJAL-629 Fasta sequence id reading whitespace fix. Flexi... tree | commitdiff
2023-01-30 Ben SoaresJAL-1988 Make sensible choices if only the opening... merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064 tree | commitdiff
2023-01-26 Ben SoaresJAL-629 adjust arg type for tempfac-shading -- was... tree | commitdiff
2023-01-24 James ProcterJAL-629 hacked in --tempfac-shading - hardcoded to... tree | commitdiff
2023-01-24 James ProcterJAL-629 suggest not breaking out of the structure proce... tree | commitdiff
2023-01-24 James ProcterJAL-629 don’t carry on Jalview.main if we’ve already... tree | commitdiff
2023-01-24 James ProcterJAL-629 don’t trash user’s system property file when... tree | commitdiff
2023-01-24 James ProcterJAL-629 don’t complain for Unary args tree | commitdiff
2023-01-24 James ProcterJAL-629 labelled breaks are frowned upon by everyone tree | commitdiff
2023-01-23 Ben SoaresJAL-629 Attempts to add PAE to structure. --headless... tree | commitdiff
2023-01-18 Ben SoaresJAL-629 make sequence id key 'seqid' tree | commitdiff
2023-01-16 Ben SoaresJAL-3416 More tweaking of FlatLaf. Problem with macOS... tree | commitdiff
2023-01-11 Ben SoaresJAL-1988 JAL-3772 Mark the _default_ STARTUP_FILE as... tree | commitdiff
2023-01-11 Ben SoaresJAL-629 refactoring TFType. Remove i18n identification... tree | commitdiff
2023-01-06 Ben SoaresJAL-3416 More explicit setting of FlatLaf macOS theme tree | commitdiff
2023-01-06 Ben SoaresJAL-3416 Upgraded FlatLaf to 3.0 and added macOS theme... tree | commitdiff
2022-12-19 Ben SoaresJAL-629 Add image output and quit tree | commitdiff
2022-12-15 Ben SoaresJAL-629 move SubId to more logical place. Attempt remov... tree | commitdiff
2022-12-14 Ben SoaresJAL-629 Open Structure Viewer from cmdline tree | commitdiff
2022-12-09 Ben SoaresJAL-629 null check, fixed tests! tree | commitdiff
2022-12-08 Ben SoaresJAL-629 stray code deleted tree | commitdiff
2022-12-08 Ben SoaresJAL-629 Allow attachment of pAE file to a particular... tree | commitdiff
2022-12-05 Ben SoaresJAL-629 implementation of --tempfac options tree | commitdiff
2022-11-23 Ben SoaresJAL-629 Doing things with the command line arguments tree | commitdiff
2022-11-16 Ben SoaresMerge branch 'improvement/JAL-3416_default_to_LIVE_DRAG... tree | commitdiff
2022-11-16 Ben SoaresJAL-3416 make flatlaf default for linux improvement/JAL-3416_default_to_LIVE_DRAG_MODE_for_flatlaf tree | commitdiff
2022-11-04 Ben SoaresJAL-1998 JAL-3772 JAL-3416 Merge conflict resolution... tree | commitdiff
2022-11-02 Ben SoaresJAL-1988 JAL-3772 Moving packages to somewhere more... tree | commitdiff
2022-11-01 Ben SoaresJAL-3416 set flatlaf default drag mode to LIVE_DRAG_MODE tree | commitdiff
2022-10-27 Ben SoaresMerge branch 'develop' into bug/JAL-1988_JAL-3772_impro... tree | commitdiff
2022-10-25 Ben SoaresJAL-3416 Making FlatLaF default for macs due to a probl... tree | commitdiff
2022-10-24 Ben SoaresJAL-1988 JAL-3772 Non-blocking modal dialogs for unsave... tree | commitdiff
2022-09-23 Ben SoaresJAL-1988 JAL-3772 Quit confirmation dialog boxes with... tree | commitdiff
2022-09-23 Ben SoaresJAL-3676 extra information about jalview_properties... tree | commitdiff
2022-08-08 Jim ProcterMerge branch 'task/JAL-3991_check_actual_JAVA_VERSION_a... tree | commitdiff
2022-06-13 Jim ProcterMerge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS... tree | commitdiff
2022-06-13 Ben SoaresJAL-3416 remove flat as default for linux tree | commitdiff
2022-06-13 Ben SoaresJAL-3416 Added some mac specific FlatLAF settings.... tree | commitdiff
2022-04-06 Ben SoaresJAL-3991 JAVA_COMPILE_VERSION put into build_properties... tree | commitdiff
2022-03-18 Ben SoaresJAL-3978 Using getdowninstanceappdir and getdowninstanc... tree | commitdiff
2022-03-18 Ben SoaresJAL-3978 New tasks to build archive 'old' dir with... tree | commitdiff
2022-03-08 Jim ProcterJAL-3746 apply copyright to source tree | commitdiff
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0 tree | commitdiff
2022-03-08 Ben SoaresJAL-3103 Removed code and unused widgets for defaultBrowser tree | commitdiff
2022-03-08 Ben SoaresJAL-3103 Remove BrowserLauncher2 and use Desktop.browse... tree | commitdiff
2022-03-07 Ben SoaresJAL-3103 Switched to (a wrapper around) BrowserLauncher2 tree | commitdiff
2022-03-04 Jim ProcterJAL-3746 JAL-3811 document SHOW_JWS2_SERVICES user... tree | commitdiff
2022-03-04 Jim ProcterJAL-3746 JAL-3812 new argument ‘-nohtmltemplates’ and... tree | commitdiff
2022-03-04 Jim ProcterJAL-3746 JAL-3813 NOIDENTIFIERSSERVICE preference disab... tree | commitdiff
2022-03-04 Jim ProcterJAL-3746 JAL-3814 NONEWS property tree | commitdiff
2022-03-02 Jim ProcterMerge branch 'benreview/JAL-3691_for_2_11_2_getdownrebu... tree | commitdiff
2022-02-17 Jim ProcterJAL-3959 add key retrieval urls that support CORS neede... tree | commitdiff
2022-02-17 Jim ProcterJAL-3691 patch toUpper/toLower to use Locale.ROOT for... tree | commitdiff
2022-02-11 Jim ProcterJAL-3949 - refactor logging from jalview.bin.Cache... tree | commitdiff
2022-02-11 Ben SoaresJAL-3949 read ~/.jalview_properties before initialising... tree | commitdiff
2022-02-11 Ben SoaresJAL-3949 Complete new abstracted logging framework... tree | commitdiff
2022-02-04 Ben SoaresJAL-3949 An attempt at converting to Log4j 2 -- no... tree | commitdiff
2022-01-28 Ben SoaresMerge branch 'develop' into JAL-3416_different_look_and... tree | commitdiff
2022-01-27 Jim ProcterMerge branch 'bug/JAL-3633_read_proxy_settings_from_jal... tree | commitdiff
2022-01-10 Ben SoaresJAL-3937 enable AIA download of intermediate certificat... tree | commitdiff
2022-01-10 Ben SoaresJAL-3937 enable AIA download of intermediate certificat... tree | commitdiff
2021-12-15 Jim ProcterJAL-3933 remove obsolete Castor logging configuration tree | commitdiff
2021-12-15 Jim ProcterJAL-3933 configure root logger console appender to... tree | commitdiff
2021-12-15 Jim ProcterJAL-3933 remove obsolete Castor logging configuration tree | commitdiff
2021-12-15 Jim ProcterJAL-3933 configure root logger console appender to... tree | commitdiff
2021-12-14 Ben SoaresJAL-3933 updated log4j and slf4j jars with log4j1.2... tree | commitdiff
2021-12-14 Ben SoaresJAL-3933 Updated log4j jars with log4j-2.16.0 and compa... tree | commitdiff
2021-10-05 Ben SoaresJAL-3416 make flat default laf for linux tree | commitdiff
2021-10-04 Ben SoaresJAL-3416 updated FlatLaf to 1.6 and added some tabbed... tree | commitdiff
2021-10-04 Ben SoaresMerge branch 'develop' into JAL-3416_different_look_and... tree | commitdiff
2021-09-21 Ben SoaresJAL-3691 automatic insertion of Locale.ROOT to toUpperC... tree | commitdiff
2021-09-15 Jim ProcterJAL-3741 http to https (and jar to jvp for exampleFile... tree | commitdiff
2021-09-14 Ben SoaresJAL-2422 More helpful highlighting/user guidance of... tree | commitdiff
2021-04-22 Ben SoaresJAL-3833 Allow setHiDPI and setHiDPIScale to work more... tree | commitdiff
2021-04-19 Ben SoaresJAL-3833 cap the scaling used by HiDPISetting for incor... tree | commitdiff
2021-04-18 Ben SoaresJAL-3833 cap the scaling used by HiDPISetting for incor... tree | commitdiff
2021-03-25 Ben SoaresJAL-3633 refactored/simplified LaunchUtils code tree | commitdiff
2021-03-20 Ben SoaresJAL-3503 Changed decimal display of memory in Prefences tree | commitdiff
2021-03-19 Ben SoaresJAL-3503 Added a Startup tab in Preferences, with gui... tree | commitdiff
2021-03-04 Ben SoaresJAL-3594 Allow a channel to use a different preferences... tree | commitdiff
2021-02-05 Jim ProcterJAL-3813 NOIDENTIFIERSSERVICE preference disables jalvi... tree | commitdiff
2021-02-05 Jim ProcterJAL-3812 new argument ‘-nohtmltemplates’ and user prefe... tree | commitdiff
2021-02-05 Jim ProcterJAL-3811 document SHOW_JWS2_SERVICES user preference... tree | commitdiff
2021-02-05 Jim ProcterJAL-3814 NONEWS property tree | commitdiff
2021-01-08 Ben SoaresJAL-3419 improved look of tabs tree | commitdiff
2021-01-08 Ben SoaresJAL-3416 Added FlatLightLaf, use with -Dlaf=flat property tree | commitdiff
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