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Merge branch 'releases/Release_2_11_4_Branch'
[jalview.git] / src / jalview / bin
10 days ago Jim ProcterMerge branch 'releases/Release_2_11_4_Branch' master commit | commitdiff
2024-08-16 Ben SoaresJAL-3631 Fix EnvConfig.getUserAppdir() in getdown when... commit | commitdiff
2024-08-05 Jim ProcterJAL-1551 source formatting and header commit | commitdiff
2024-08-05 Jim ProcterJAL-1551 gradle spotlessApply and doc tweaks commit | commitdiff
2024-07-31 Ben SoaresJAL-3631 Changes to Getdown to call getdown-launcher... commit | commitdiff
2024-07-29 Ben SoaresJAL-3631 Add PID to console info - only available in... commit | commitdiff
2024-07-26 Ben SoaresJAL-3631 Added an --update option to the jalview.sh... commit | commitdiff
2024-06-28 Ben SoaresJAL-3631 Change in user path for locally installed... commit | commitdiff
2024-06-27 Ben SoaresJAL-3631 Add property to let log4j know we're not runni... commit | commitdiff
2024-06-27 Ben SoaresJAL-3631 Log4j logging to .jalview.log file when reques... commit | commitdiff
2024-06-25 Ben SoaresJAL-3631 JAL-3384 Install4j launch now redirects STDOUT... commit | commitdiff
2024-06-24 Ben SoaresJAL-3631 Report getCanonicalPath for installer appdir commit | commitdiff
2024-06-21 Ben SoaresJAL-3631 Changed label for consistency commit | commitdiff
2024-06-19 Ben SoaresJAL-3631 Rename/rationalise informational system proper... commit | commitdiff
2024-06-18 Ben SoaresJAL-3631 Substantial additions to Getdown (through... commit | commitdiff
2024-06-14 Ben SoaresJAL-3631 JAL-4104 More consistent system property names... commit | commitdiff
2024-06-13 Ben SoaresJAL-3845 Add a popup error message, with instructions... commit | commitdiff
2024-06-12 Ben SoaresJAL-3631 Name changes to system properties and a fallba... commit | commitdiff
2024-06-04 Jim ProcterMerge branch 'releases/Release_2_11_3_Branch' commit | commitdiff
2024-05-29 Ben SoaresJAL-4409 Allow more URI schemes (e.g. file) to be opene... commit | commitdiff
2024-05-29 Ben SoaresJAL-4414 Add SocketTimeoutException to exceptions that... commit | commitdiff
2024-05-27 Ben SoaresMerge branch 'develop' into improvement/JAL-4409_implem... commit | commitdiff
2024-05-21 Ben SoaresJAL-1054 Change one more (unused) url.openStream to... commit | commitdiff
2024-05-21 Ben SoaresJAL-4409 Make HttpUtils.equivalentJalviewUrlString... commit | commitdiff
2024-05-20 Ben SoaresJAL-4409 Also interpret jalviewX:// URIs in Jalview... commit | commitdiff
2024-05-17 Ben SoaresJAL-4420 Add some debugging statements commit | commitdiff
2024-05-17 Ben SoaresJAL-4420 Allow preprocessing of arguments if they are... commit | commitdiff
2024-05-15 Ben SoaresJAL-4409 Refactoring to allow easier reuse of classes... commit | commitdiff
2024-05-14 Ben SoaresJAL-4414 Add a FileNotFoundException when identifying... commit | commitdiff
2024-05-13 Ben SoaresJAL-1054 Fix wrappers for following http->https redirects commit | commitdiff
2024-05-13 Ben SoaresJAL-1054 Add wrappers for URL.openConnection(), URL... commit | commitdiff
2024-04-30 Renia CorreyaJAL-4392 Merging consensus secondary structure commit | commitdiff
2024-01-23 James ProcterMerge branch 'develop' into bug/JAL-4290_headless_align... commit | commitdiff
2024-01-23 James ProcterJAL-4369 invokeAndWait to avoid hang whilst calling... commit | commitdiff
2024-01-23 James ProcterMerge branch 'bug/JAL-4373_jvmmemmax_and_jvmmempc_ignor... commit | commitdiff
2024-01-19 Ben SoaresJAL-4373 Setting the jvmmempc and jvmmemmax strings... bug/JAL-4373_jvmmemmax_and_jvmmempc_ignored_on_command_line_for_executable_jar_launch commit | commitdiff
2024-01-05 Ben SoaresJAL-4368 Only set a colour scheme if --colour is given... bug/JAL-4368_default_colourscheme_applied_to_JVP_inappropriately commit | commitdiff
2023-12-19 Ben SoaresJAL-4290 Fixed one test commit | commitdiff
2023-12-18 Ben SoaresJAL-4290 incorrect usage of main() commit | commitdiff
2023-12-15 Ben SoaresJAL-4290 Add method to allow for specific settings... commit | commitdiff
2023-12-15 Ben SoaresJAL-4290 Set structureSelectionManager settings more... commit | commitdiff
2023-12-15 Ben SoaresJAL-4290 Move some annotation visibility settings to... commit | commitdiff
2023-12-12 Ben SoaresJAL-4353 helper method and test for primary/secondary... commit | commitdiff
2023-12-06 Ben SoaresJAL-4353 Preserve the user given 'linkedId' with ArgVal... commit | commitdiff
2023-12-05 Ben SoaresJAL-4353 Add secondary Types for Args, for STRUCTUREIMA... commit | commitdiff
2023-12-01 James ProcterMerge branch 'releases/Release_2_11_3_Branch' commit | commitdiff
2023-11-30 Ben SoaresJAL-4344 careful application of -Djava.awt.headless... commit | commitdiff
2023-11-16 James ProcterMerge branch 'releases/Release_2_11_3_Branch' commit | commitdiff
2023-11-13 James ProcterJAL-4090 JAL-1551 source license commit | commitdiff
2023-11-03 James ProcterJAL-4090 JAL-1551 spotlessApply commit | commitdiff
2023-11-02 James ProcterJAL-4217 wrap progress bar creation in an invokeLater... commit | commitdiff
2023-10-25 James ProcterJAL-4312 call AlignFrame.setAnnotationsVisibility on... commit | commitdiff
2023-10-20 James ProcterMerge branch 'improvement/JAL-3783_upgrade_to_groovy... commit | commitdiff
2023-10-20 Ben SoaresJAL-4298 Remove a stray return in the processGroovyScri... commit | commitdiff
2023-10-19 Ben SoaresJAL-629 Fix --nodebug turning off debug mode from prope... commit | commitdiff
2023-10-19 Ben SoaresJAL-4305 Isolate and unify the Jalview object from... commit | commitdiff
2023-10-18 Ben SoaresJAL-629 Run non-alignframe linked groovy scripts. ... commit | commitdiff
2023-10-11 Ben SoaresJAL-629 correct a timeout. Correct passing html flag. commit | commitdiff
2023-10-11 Ben SoaresJAL-629 Add a timeout to modal dialogs for command... commit | commitdiff
2023-10-11 Ben SoaresJAL-629 Remove argfiles from the hashset of used argfil... commit | commitdiff
2023-10-11 Ben SoaresJAL-4298 Added diagnostics and minor dimension changes... commit | commitdiff
2023-10-05 Ben SoaresJAL-4298 Fixed initial log level to see .jalview_proper... commit | commitdiff
2023-09-29 James ProcterJAL-629 JAL-4265 JAL-4286 report the filename for the... commit | commitdiff
2023-09-21 Ben SoaresJAL-4265 Use ColourUtils.parseColourString() for consis... merge/JAL-4262+JAL-4265+JAL-4269+JAL-4274+JAL-4277+JAL-4285 commit | commitdiff
2023-09-21 Ben SoaresMerge branch 'develop' into merge/JAL-4262+JAL-4265... commit | commitdiff
2023-09-20 Ben SoaresJAL-4265 Use ColorUtils.parseColourString() and adjust... commit | commitdiff
2023-09-20 James ProcterJAL-4285 don’t say you are reporting warnings/errors... commit | commitdiff
2023-09-20 James ProcterJAL-4265 JAL-4286 reinstated explicit restoreSession... commit | commitdiff
2023-09-20 James ProcterJAL-4195 JAL-1069 JAL-4160 errors in Cache should go... commit | commitdiff
2023-09-20 James ProcterJAL-4265 bail early when attempting to export a view... commit | commitdiff
2023-09-19 Ben SoaresJAL-4265 Change to use JmolCommands commit | commitdiff
2023-09-19 Ben SoaresJAL-629 Allow multiple structure images for multiple... commit | commitdiff
2023-09-16 Ben SoaresJAL-629 Fix a test and omit an incorrect error message... improvement/JAL-4269_reduce_variants_of_common_subvalue_parameters commit | commitdiff
2023-09-16 Ben SoaresJAL-4265 Added --bgcolour for --structureimage output... commit | commitdiff
2023-09-16 Ben SoaresJAL-4269 Now using --width, --height, --scale for both... commit | commitdiff
2023-09-14 Ben SoaresMerge branch 'develop' into feature/JAL-4274_configurab... commit | commitdiff
2023-09-13 Ben SoaresJAL-4274 Use Cache BITMAP_* if no other image restricti... commit | commitdiff
2023-09-13 Ben SoaresJAL-4262 Made deprecation warning properly modal bug/JAL-4277_dirname_substitution_always_absolute commit | commitdiff
2023-09-12 Ben SoaresJAL-4262 Allow HTML in the dialog box for link to CLI... commit | commitdiff
2023-09-12 Ben SoaresJAL-4285 Better checkFiles processing. Better dialog. commit | commitdiff
2023-09-12 Ben SoaresJAL-4285 JAL-4262 Added a scrollable dialog to display... commit | commitdiff
2023-09-11 Ben SoaresJAL-4001 corrected analytics message labels commit | commitdiff
2023-09-11 Ben SoaresMerge branch 'improvement/JAL-4262_deprecation_warning_... commit | commitdiff
2023-09-11 Ben SoaresJAL-4277 --mkdirs with cautious refusal for paths with .. commit | commitdiff
2023-09-11 Ben SoaresJAL-4284 JAL-4285 Deal with output files/images consist... commit | commitdiff
2023-09-08 Ben SoaresJAL-4262 Make an excepetion for STDOUT filename in... improvement/JAL-4262_deprecation_warning_when_old_CLI_arguments_are_processed commit | commitdiff
2023-09-08 Ben SoaresMerge branch 'bug/JAL-4277_dirname_substitution_always_... commit | commitdiff
2023-09-08 Ben SoaresJAL-4262 Dialog for GUI and WARN for CLI of old style... commit | commitdiff
2023-09-07 Ben SoaresMerge branch 'develop' into bug/JAL-4277_dirname_substi... commit | commitdiff
2023-09-07 Ben SoaresJAL-4277 Corrected choice of all or last opened linkedI... commit | commitdiff
2023-09-07 James ProcterJAL-4279 suppress error dialogs raised by file loader... improvement/JAL-4279_gracefully_handle_failure_to_openviaCLI commit | commitdiff
2023-09-07 James ProcterJAL-4279 move on if the file doesn't exist, or Identify... commit | commitdiff
2023-09-07 James ProcterJAL-4279 catch exceptions with fileLoader and report... commit | commitdiff
2023-09-07 James ProcterJAL-4090 JAL-4160 JAL-4274 image export dimensions... commit | commitdiff
2023-09-07 Ben SoaresJAL-629 Change names of Opt.ALLOWALL to Opt.ALLOWMULTII... improvement/JAL-629_Apply_alignment_options_to_all_globbed_files commit | commitdiff
2023-09-06 James ProcterJAL-629 javadoc commit | commitdiff
2023-09-02 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_t... commit | commitdiff
2023-09-02 Ben SoaresJAL-629 Add accessors for argParser and bootstrapArgs feature/JAL-629_--output_-_means_output_to_STDOUT commit | commitdiff
2023-09-01 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_t... commit | commitdiff
2023-09-01 Ben SoaresJAL-629 Fix --structureimage and options commit | commitdiff
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