JAL-629 Change behaviour of --open GLOB to increment defaultLinkedId to allow --allfr...
[jalview.git] / src / jalview / bin /
2020-07-07 Ben SoaresJAL-3608 Changes from code review CR-JAL-236
2020-07-07 Ben SoaresJAL-3608 ex stacktraces now go to Cache.log.debug
2020-07-07 Ben SoaresJAL-3628 System.out/err -> Cache.log.info/error
2020-07-07 Ben SoaresMerge branch 'bug/JAL-3628_Unable_to_save_update_to_exi...
2020-07-07 Ben SoaresJAL-3628 System.out/err -> Cache.log.info/error
2020-07-07 Ben SoaresJAL-3628 Fixed oddly worded and non-formatted error...
2020-07-01 Ben SoaresMerge branch 'task/JAL-3608_property_set_laf_and_tests_...
2020-06-26 Jim ProcterJAL-3671 hardwire log4j.root logger to INFO to supress...
2020-06-21 Ben SoaresJAL-3609 Report when scale setting used.
2020-06-21 Ben SoaresJAL-3609 New auto-scale 'formula' for linux HiDPI....
2020-06-16 Ben SoaresJAL-3608 non-JS cherry-pick
2020-06-16 Jim ProcterMerge branch 'bug/JAL-3561_translatefileformats' into... patch/JAL-3561_JAL-3660_fileformatexport_CLI
2020-06-16 Jim ProcterJAL-3660 JAL-3561 output alignment as requested file... bug/JAL-3561_translatefileformats
2020-06-16 Ben SoaresJAL-3608 formatting save only
2020-06-16 Ben SoaresJAL-3608 formatting save only
2020-05-22 soaresJAL-3609 corrected maxdimension to mindimension. Adjust...
2020-05-20 Ben SoaresJAL-3609 removed debugging prints
2020-05-19 Ben SoaresJAL-3609 changed property names to something more palat...
2020-05-19 Ben SoaresJAL-3609 system properties to force a scale, or automat...
2020-05-19 Ben SoaresJAL-3609 Added a -DforceHiDPISetting=true option mainly...
2020-05-18 gmungocMerge branch 'Jalview-JS/develop' into develop
2020-05-15 Ben SoaresJAL-3609 HiDPI scale setting done via system prop in...
2020-05-04 Ben SoaresJAL-3608 streamlined LaF methods and allow specificying...
2020-05-03 Ben SoaresJAL-3608 also look at user pref PREFERRED_LAF
2020-05-01 Ben SoaresJAL-3608 Now reporting the actual LookAndFeel in Java...
2020-05-01 Ben SoaresJAL-3608 Added java builtin NimbusLookAndFeel option...
2020-04-30 Ben SoaresJAL-3608 Enforcing MetalLookAndFeel as default on linux...
2020-04-30 Ben SoaresJAL-3608 Added 'metal' option for laf property
2020-04-23 soaresJAL-3608 JAL-3416 Added a 'gtk' option. Not currently...
2020-04-22 soaresJAL-3608 saved in Eclipse with auto formatting
2020-04-22 Ben SoaresJAL-3608 Added CrossPlatform LaF and made configurable...
2020-04-21 Jim ProcterJAL-3407 add GPL license to Jalview source files
2020-03-30 gmungocMerge branch 'develop' into Jalview-JS/develop
2020-02-27 Ben SoaresJAL-3543 remove debugging output improvement/JAL-3543_dont_report_null_versions_in_java_console
2020-02-27 Ben SoaresMerge branch 'develop' into improvement/JAL-3543_dont_r...
2020-02-27 Ben SoaresJAL-3543 Conditional reporting of Install4j and Getdown...
2020-02-26 Jim ProcterMerge branch 'bug/JAL-3477_memory_max_allocation' into...
2020-01-10 Ben SoaresJAL-3477 Javadoc, addition of -jvmmempc and -jvmmemmax...
2020-01-09 Ben SoaresJAL-3477 Refactoring based on CR-JAL-189
2020-01-09 Ben SoaresJAL-3477 Javadoc, refactoring and slight changes to...
2019-12-06 Ben SoaresJAL-3449 Added more versions to getdown splashscreen...
2019-11-22 Ben SoaresJAL-3449 install4j version, install4j template version...
2019-11-20 Ben SoaresJAL-3477 A bit of refactoring for the better
2019-11-19 Ben SoaresJAL-3210 removing overly complicated logging. Settling...
2019-11-18 Ben SoaresJAL-3477 New jvmmemmax config option in getdown and...
2019-11-18 Ben SoaresJAL-3477 New sensible default decisions on memory,...
2019-11-12 gmungocJAL-3274 resource path correction, code tidying (consta...
2019-11-05 gmungocJAL-3210 JAL-3130 skip Taskbar in JalviewJS
2019-11-05 gmungocJAL-3210 JAL-3330 use SequenceOntologyLite in JalviewJS
2019-07-16 gmungocJAL-3210 Merge branch 'develop' into trialMerge
2019-07-02 Jim ProcterMerge branch 'develop' into tasks/JAL-3311_removeVamsasMenu
2019-06-26 Jim ProcterJAL-3334 fix - always load full SO to resolve the seque...
2019-06-26 Jim ProcterJAL-3111 get rid of nasty tab characters
2019-06-19 Ben SoaresJAL-3321 Last pieces of the getdown-launcher.jar upgrad...
2019-06-17 Ben SoaresJAL-3310 JAL-3300 two getdown fixes merged
2019-06-17 Jim ProcterJAL-3311 remove menus and documentation relating to... tasks/JAL-3311_removeVamsasMenu
2019-06-14 Ben SoaresJAL-3278 A system.out.println turned into a cache.log...
2019-06-14 Jim ProcterJAL-3111 report build type and commit in stdout from...
2019-06-14 Jim ProcterJAL-3299 JAL-3280 javadoc on BuildDetails bean
2019-05-22 Jim ProcterJAL-3274 import build properties and authors resources... Jalview-JS/tasks/JAL-3274-build_details
2019-05-21 Ben SoaresJAL-3247 Launcher start improvements. RPM and DEB no...
2019-05-20 Ben SoaresJAL-3254 Improved memory setting (allows mem for OS...
2019-04-26 Ben SoaresJAL-3233 Added isAMac check for -Xdock:icon addition...
2019-04-25 Ben SoaresJAL-3224 JAL-3225 Some fixes in install4j template...
2019-04-25 Ben SoaresJAL-3224 JAL-3225 Added lines to check for updates...
2019-04-24 Jim ProcterMerge branch 'task/JAL-3225_Integration_Gradle_building...
2019-04-15 Ben SoaresJAL-3130 Helper classes to take Class Exceptions when...
2019-04-05 hansonrfixes for Jalview command-line URI code
2019-04-03 hansonrreplacing @j2sNative with @j2sIgnore where appropriate...
2019-04-03 hansonrj2sNative clean-up. Fixes problem with second try of...
2019-04-01 Ben SoaresJAL-3130 JAL-3007 Added gradle build for Java 11 and...
2019-03-31 hansonrCache JS adds search of Info for jalview_xxx properties
2019-03-27 gmungocJAL-3032 small formatting and isJS() tidy
2019-03-27 hansonrreinstating test data for JalviewJS
2019-03-27 hansonrcomment out of @j2sNative block
2019-03-27 hansonrconsolidation of Platform isJS calls
2019-03-27 hansonrisJS cleanup
2019-03-20 Ben SoaresJAL-3130 Lots of deprecation fixes. See utils/deprecat...
2019-03-13 gmungocMerge branch 'develop' into trialMerge
2019-03-11 gmungocMerge branch 'feature/JAL-3127_seqidChainshading' into...
2019-03-06 gmungocMerge branch 'tasks/JAL-3035_remove_dasobert_dependency...
2019-03-06 gmungocJAL-3035 more das bits removed
2019-03-06 Jim ProcterJAL-3208 re-enable the setprop CLI arg, but only in...
2019-03-04 gmungocMerge remote-tracking branch 'origin/tasks/JAL-3035_rem...
2019-02-28 gmungocJAL-3032 any url parameter not "j2s..." taken as Jalvie... Jalview-BH/JAL-3026-JAL-3063-JAXB
2019-02-25 gmungocJAL-3032 Jalview (as JS) parse query params to main...
2019-02-25 gmungocJAL-3032 JalviewJS2 converts url query parameters to...
2019-01-26 hansonrJalview.isJS() --> Platform.isJS(), DBRefEntry[] -...
2019-01-21 hansonrisAMac() -> isAMacAndNotJS(), isWindows() -> isWindowsA...
2019-01-18 hansonrcanvas line/font/pixel fixes; menu accelerators;
2019-01-11 hansonr(commented out but potentially useful) methods to tap...
2018-12-01 hansonradding jaxbtest.jvx and directing JalviewJS2.java to...
2018-11-11 hansonradds static declaration of AJAX-readable domains
2018-10-19 Ben SoaresJAL-3141 Backup files being created with default suffix...
2018-10-17 Jim ProcterMerge branch 'feature/JAL-3063JAXB' into Jalview-BH...
2018-10-09 Jim ProcterJAL-3127 pass reference to AlignViewportI when creating...
2018-09-18 Jim ProcterJAL-3035 more dedasification
2018-09-11 Jim ProcterMerge branch 'develop' into releases/Release_2_11_Branch
2018-09-05 Jim ProcterJAL-3065 - amended commit 4906697ab6e5a79fbce3baae89f7... bug/JAL-3065_DH_keyPair_Exception_nogroovysettings
2018-08-21 hansonrmc_view references were MCview
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