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Merge branch 'releases/Release_2_11_4_Branch'
[jalview.git] / src
3 days ago Jim ProcterMerge branch 'releases/Release_2_11_4_Branch' master commit | commitdiff
4 days ago Jim ProcterJAL-4414 JAL-1054 fix irrelevant failing network test... commit | commitdiff
4 days ago Jim ProcterMerge branch 'bug/JAL-1054_broken_test' into develop commit | commitdiff
4 days ago Jim ProcterMerge branch 'JAL-4442_cant_quit_jalview_on_windows_11... commit | commitdiff
4 days ago Jim ProcterJAL-4418 JAL-4392 show/hide group associated secondary... commit | commitdiff
4 days ago Jim ProcterMerge branch 'improvement/JAL-4461_select_format_from_e... commit | commitdiff
5 days ago Jim ProcterJAL-4392 JAL-4425 commented out code to allow consensus... commit | commitdiff
5 days ago Jim ProcterMerge branch 'patch/JAL-4392_hide_ssconsensus_if_no_dat... commit | commitdiff
5 days ago Jim ProcterMerge branch 'bug/JAL-4427_HTML_code_in_sequence_ID_tex... commit | commitdiff
5 days ago Jim ProcterJAL-4392 autohide the secondary structure consensus... patch/JAL-4392_hide_ssconsensus_if_no_data commit | commitdiff
5 days ago Renia CorreyaJAL-4427 Added test cases and a minor correction bug/JAL-4427_HTML_code_in_sequence_ID_text commit | commitdiff
5 days ago Jim ProcterJAL-4392 don't show SS consensus for DNA alignments commit | commitdiff
5 days ago Ben SoaresJAL-4461 Move SwingUtils to darrylbu.util.SwingUtils... improvement/JAL-4461_select_format_from_extension commit | commitdiff
8 days ago Jim ProcterMerge branch 'improvement/JAL-4461_select_format_from_e... commit | commitdiff
8 days ago Ben SoaresJAL-4461 Tests for JalviewFileChooser.defaultSaveFileFo... commit | commitdiff
8 days ago Ben SoaresJAL-4461 Adding in a number of properties that control... commit | commitdiff
8 days ago Ben SoaresJAL-4461 Change JalviewFileFilter to use LinkedHashSet... commit | commitdiff
9 days ago Jim ProcterMerge branch 'bug/JAL-4427_HTML_code_in_sequence_ID_tex... commit | commitdiff
9 days ago Ben SoaresJAL-4461 Added a dynamic tooltip to give more informati... commit | commitdiff
9 days ago Jim ProcterJAL-4461 fix up formatting and remove old comment commit | commitdiff
9 days ago Jim ProcterJAL-4461 after autodetection, update the filechooser... commit | commitdiff
9 days ago Ben SoaresJAL-4461 Change labelling of All-known-alignment-files... commit | commitdiff
9 days ago Ben SoaresJAL-4460 Don't display the All-known-alignment-files... bug/JAL-4460_alignment_save_as_format_not_registering commit | commitdiff
10 days ago Ben SoaresJAL-4460 In save as, set format from file extension... commit | commitdiff
10 days ago Ben SoaresJAL-4460 Don't add .aln for an 'All known formats.... commit | commitdiff
10 days ago Ben SoaresJAL-4460 Update currentFileFormat /after/ new format... commit | commitdiff
2024-09-03 Jim ProcterJAL-4386 remove magic string in registerScoreModel... commit | commitdiff
2024-09-02 Ben SoaresJAL-1054 Add option to always follow redirects and... bug/JAL-1054_broken_test commit | commitdiff
2024-08-30 Renia CorreyaFix for JAL-4427 commit | commitdiff
2024-08-29 Jim ProcterJAL-4446 improved reporting of progress, and transition... feature/JAL-4446_cancellable_pasimap_etal commit | commitdiff
2024-08-29 Jim ProcterJAL-4446 refactor progress listener handler code for... commit | commitdiff
2024-08-29 Jim ProcterMerge branch 'develop' into feature/JAL-4446_cancellabl... commit | commitdiff
2024-08-28 Jim ProcterMerge branch 'feature/JAL-3631_allow_jalview_to_work_fr... commit | commitdiff
2024-08-26 Jim ProcterJAL-4420 new drag'n'drop behaviour is now an 'Experimen... commit | commitdiff
2024-08-26 Jim ProcterJAL-4420 report exceptions raised during a drop rather... commit | commitdiff
2024-08-26 Ben SoaresJAL-4442 Removed debugging variables and a stray 'wait... JAL-4442_cant_quit_jalview_on_windows_11 commit | commitdiff
2024-08-26 Jim ProcterMerge branch 'bug/JAL-4398_Window_menu_font_rendering... commit | commitdiff
2024-08-26 Jim ProcterMerge branch 'develop' into JAL-4442_cant_quit_jalview_... commit | commitdiff
2024-08-23 Jim ProcterJAL-4449 signed off and also updated Ensembl REST API... commit | commitdiff
2024-08-22 Ben SoaresJAL-4449 Changed HttpUtils.followConnection(conn0)... commit | commitdiff
2024-08-21 Jim ProcterJAL-4442 reprioritise QuitHandler debug output to eithe... commit | commitdiff
2024-08-21 Jim ProcterJAL-4442 reprioritise JvOptionPane debug output to... commit | commitdiff
2024-08-19 Jim ProcterJAL-789 limit applicable score models to substitution... commit | commitdiff
2024-08-19 Jim ProcterJAL-4446 allow progress bar to become indeterminate... commit | commitdiff
2024-08-19 Jim ProcterMerge branch 'develop' into feature/JAL-4446_cancellabl... commit | commitdiff
2024-08-16 Ben SoaresJAL-3631 Fix EnvConfig.getUserAppdir() in getdown when... commit | commitdiff
2024-08-12 Ben SoaresJAL-4442 Add a wait for termination of button action... commit | commitdiff
2024-08-07 Jim ProcterJAL-4447 standardised title formula for reporting score... commit | commitdiff
2024-08-07 Jim ProcterJAL-4446 reuse lasteta value commit | commitdiff
2024-08-07 Jim ProcterJAL-4159 JAL-789 report pasimap and pairwise alignment... commit | commitdiff
2024-08-07 Jim ProcterJAL-4159 suppress pairwise alignment display options... commit | commitdiff
2024-08-07 Jim ProcterJAL-4446 better reporting of ETA estimation - particula... commit | commitdiff
2024-08-06 Jim ProcterJAL-4446 avoid NPE when progress bar message is null commit | commitdiff
2024-08-05 Jim ProcterJAL-1551 source formatting and header commit | commitdiff
2024-08-05 Jim ProcterJAL-4446 .. missing methods for cancellable pasimap commit | commitdiff
2024-08-05 Jim ProcterJAL-4446 cancellable Pasimap - still need to make the... commit | commitdiff
2024-08-05 Jim ProcterJAL-4446 calculate and report PaSiMap ETA in progress bar commit | commitdiff
2024-08-05 Jim ProcterJAL-4446 allow progress bar message to be changed whils... commit | commitdiff
2024-08-05 Jim ProcterJAL-1551 apply GPLv3 for source files commit | commitdiff
2024-08-05 Jim ProcterJAL-1551 gradle spotlessApply and doc tweaks commit | commitdiff
2024-08-01 Jim ProcterMerge branch 'feature/JAL-3631_allow_jalview_to_work_fr... 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
2024-07-29 Jim ProcterJAL-4443 patch out pasimap in GUI for JalviewJS and... commit | commitdiff
2024-07-26 Ben SoaresJAL-3631 Added an --update option to the jalview.sh... commit | commitdiff
2024-07-01 Ben SoaresJAL-3631 Harden defence against looping getdown relaunc... 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
2024-06-25 Ben SoaresJAL-3631 Change parity of comparison for convention commit | commitdiff
2024-06-24 Ben SoaresJAL-3631 Report getCanonicalPath for installer appdir commit | commitdiff
2024-06-24 Ben SoaresJAL-3631 Check Implementation-Version of getdown-launch... commit | commitdiff
2024-06-21 Ben SoaresJAL-3631 Changed label for consistency commit | commitdiff
2024-06-21 Ben SoaresJAL-4409 Add two empty args to getdown call from instal... 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
2024-06-07 Ben SoaresMerge branch 'develop' into improvement/JAL-4409_implem... commit | commitdiff
2024-06-06 Ben SoaresJAL-4420 Added some more filename extensions commit | commitdiff
2024-06-06 Ben SoaresJAL-4358 Add the JALVIEW: CREATED DESKTOP line to java... commit | commitdiff
2024-06-05 Ben SoaresJAL-4420 Allow associated files to be dragged on separa... commit | commitdiff
2024-06-05 Ben SoaresJAL-4409 Small refactoring of ArgParserUtils to allow... commit | commitdiff
2024-06-05 Ben SoaresMerge branch 'develop' into bug/JAL-4421_customise_volu... commit | commitdiff
2024-06-04 Jim ProcterMerge branch 'improvement/JAL-4409_implement_extra_sche... 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-4409 Allow more URI schemes (e.g. file) to filter... commit | commitdiff
2024-05-29 Ben SoaresJAL-4414 Add SocketTimeoutException to exceptions that... commit | commitdiff
2024-05-28 Ben SoaresJAL-4409 JAL-4160 Don't let getdown turn jalviewX:... commit | commitdiff
2024-05-28 Ben SoaresJAL-4409 Don't insist on HttpURLConnection, allows... commit | commitdiff
2024-05-27 Ben SoaresMerge branch 'develop' into improvement/JAL-4409_implem... commit | commitdiff
2024-05-24 Jim ProcterJAL-4159 fix PairwiseAlignmentPanelTest - reinstate... commit | commitdiff
2024-05-24 Jim ProcterJAL-4159 peek in a Jalview project's PCA viewer's title... commit | commitdiff
2024-05-24 Jim ProcterJAL-4257 JAL-4159 JAL-789 tidy up passing of score... commit | commitdiff
2024-05-24 James ProcterJAL-789 pairwise alignment via calculations dialog... commit | commitdiff
2024-05-24 James ProcterJAL-4366 compute coverage on each side of the pairwise... commit | commitdiff
2024-05-24 Jim ProcterMerge branch 'jims/feature/JAL-4159_pasimap' into featu... commit | commitdiff
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