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2023-03-28	Ben Soares	JAL-629 Opening files in new windows. not working yet	commit \| commitdiff \| tree
2023-03-25	Ben Soares	JAL-629 open initial non-Arg arguments as files in...	commit \| commitdiff \| tree
2023-03-25	Ben Soares	JAL-629 improvements to argparser toString. Improvements...	commit \| commitdiff \| tree
2023-03-24	Ben Soares	Merge branch 'develop' into features/r2_11_2_alphafold...	commit \| commitdiff \| tree
2023-03-24	Ben Soares	JAL-629 Test tidyup	commit \| commitdiff \| tree
2023-03-23	Ben Soares	JAL-629 don't clear appProps in tests	commit \| commitdiff \| tree
2023-03-23	Ben Soares	JAL-629 refactor ArgParser and helper classes all to...	commit \| commitdiff \| tree
2023-03-21	Ben Soares	JAL-629 null checks for Desktop.instance.closeAll(...	commit \| commitdiff \| tree
2023-03-18	Ben Soares	JAL-629 restore original tests memory settings	commit \| commitdiff \| tree
2023-03-18	Ben Soares	JAL-629 restore original tests memory settings	commit \| commitdiff \| tree
2023-03-18	Ben Soares	JAL-629 Check for new commandsSuccess before quit	commit \| commitdiff \| tree
2023-03-18	Ben Soares	JAL-629 move getdown update to earlier stage	commit \| commitdiff \| tree
2023-03-18	Ben Soares	JAL-629 Back to forking tests	commit \| commitdiff \| tree
2023-03-17	Ben Soares	JAL-629 All applications System.exits going through...	commit \| commitdiff \| tree
2023-03-17	Ben Soares	JAL-629 whittling down options for successful tests	commit \| commitdiff \| tree
2023-03-17	Ben Soares	JAL-629 whittling down options for successful tests	commit \| commitdiff \| tree
2023-03-17	Ben Soares	JAL-629 whittling down options for successful tests	commit \| commitdiff \| tree
2023-03-17	Ben Soares	JAL-629 whittling down options for successful tests	commit \| commitdiff \| tree
2023-03-17	Ben Soares	JAL-629 more memory to tests task	commit \| commitdiff \| tree
2023-03-17	Ben Soares	JAL-629 add in jvmArgs for memory for tests and keep...	commit \| commitdiff \| tree
2023-03-17	Ben Soares	JAL-629 remove jvmArgs for memory for tests. Increase...	commit \| commitdiff \| tree
2023-03-17	Ben Soares	JAL-629 Add in jvmArgs for memory for tests	commit \| commitdiff \| tree
2023-03-16	Ben Soares	JAL-629 closer to normal gradle settings with just...	commit \| commitdiff \| tree
2023-03-16	Ben Soares	JAL-629 increase test JVM size	commit \| commitdiff \| tree
2023-03-16	Ben Soares	JAL-629 failFast and new threads for each test	commit \| commitdiff \| tree
2023-03-16	Ben Soares	JAL-629 increased memory for clover	commit \| commitdiff \| tree
2023-03-16	Ben Soares	Merge branch 'features/r2_11_2_alphafold/JAL-629' into...	commit \| commitdiff \| tree
2023-03-16	Ben Soares	JAL-629 revert metal laf	commit \| commitdiff \| tree
2023-03-16	Ben Soares	JAL-629 Set Metal as default LAF for build server tests	commit \| commitdiff \| tree
2023-03-16	Ben Soares	JAL-629 fixed a test failing when run without a Jalview...	commit \| commitdiff \| tree
2023-03-15	Ben Soares	JAL-3833 fixed HiDPI test for macOS	commit \| commitdiff \| tree
2023-03-15	Ben Soares	JAL-629 Commands more objecty, less classy. FileLoader...	commit \| commitdiff \| tree
2023-03-13	Ben Soares	JAL-629 teardown in CommandsTest	commit \| commitdiff \| tree
2023-03-12	Ben Soares	JAL-629 Allow substitutions of {} = defaultCounter...	commit \| commitdiff \| tree
2023-03-11	Ben Soares	JAL-629 --substitutions --nosubstitutions flags, -...	commit \| commitdiff \| tree
2023-03-11	Ben Soares	JAL-629 Auto and Default count incrementer args. Flags...	commit \| commitdiff \| tree
2023-03-11	Ben Soares	JAL-629 start of CommandsTest. More ArgParserTests.	commit \| commitdiff \| tree
2023-03-10	Ben Soares	JAL-629 start of tests and more examples	commit \| commitdiff \| tree
2023-03-09	Ben Soares	JAL-629 start of tests	commit \| commitdiff \| tree
2023-03-09	Ben Soares	JAL-629 --argfile=glob implemented. Remove reference...	commit \| commitdiff \| tree
2023-03-08	Ben Soares	JAL-629 --close individually for each AlignFrame opened...	commit \| commitdiff \| tree
2023-03-08	Ben Soares	JAL-629 improved comment and return speed of StringUtils...	commit \| commitdiff \| tree
2023-03-08	Ben Soares	JAL-629 --quiet [no stdout], --quiet --quiet [no stderr...	commit \| commitdiff \| tree
2023-03-08	Ben Soares	JAL-629 Fix --headless for new args. Fix progressbar...	commit \| commitdiff \| tree
2023-03-08	Ben Soares	JAL-629 stash some TFType and PAEFile info into a PDBEntry	commit \| commitdiff \| tree
2023-03-06	Ben Soares	JAL-629 Fix null AlignPanel. More descriptive label...	commit \| commitdiff \| tree
2023-03-03	Ben Soares	JAL-629 Improved consistency of ArgParser classes ...	commit \| commitdiff \| tree
2023-03-02	Ben Soares	JAL-629 slight tidy up	commit \| commitdiff \| tree
2023-03-02	Ben Soares	JAL-629 Removal of unnecessary methods. Set pLTTD tempfac...	commit \| commitdiff \| tree
2023-03-02	Ben Soares	JAL-629 Some refactoring to allow more flexible use...	commit \| commitdiff \| tree
2023-02-28	Ben Soares	JAL-629 Firm up bootstrapArgs. Correct '-colour' in...	commit \| commitdiff \| tree
2023-02-27	Ben Soares	JAL-629 add AF examples for FER1_SPIOL. Link and display...	commit \| commitdiff \| tree
2023-02-27	Ben Soares	JAL-629 Fix Exceptions when running with CLI not headless	commit \| commitdiff \| tree
2023-02-27	Ben Soares	JAL-629 Guesstimate whether to set pLDDT with PDB file	commit \| commitdiff \| tree
2023-02-27	Ben Soares	JAL-629 JAL-4124 JAL-3855 remove deleted debugging...	commit \| commitdiff \| tree
2023-02-27	Ben Soares	Merge branch 'develop' into features/r2_11_2_alphafold...	commit \| commitdiff \| tree
2023-02-27	Ben Soares	JAL-629 removed debug prints. added .cif. added some...	commit \| commitdiff \| tree
2023-02-26	Ben Soares	JAL-629 PAE matrix file guesstimate from filename	commit \| commitdiff \| tree
2023-02-24	Ben Soares	JAL-629 Position GUI widgets for PDF file options....	commit \| commitdiff \| tree
2023-02-24	Ben Soares	Merge branch 'develop' into features/r2_11_2_alphafold...	commit \| commitdiff \| tree
2023-02-24	Ben Soares	JAL-629 add widgets to StructureChooser for tempfac...	commit \| commitdiff \| tree
2023-02-24	Ben Soares	JAL-629 helper function for getting sensible structure...	commit \| commitdiff \| tree
2023-02-24	Ben Soares	JAL-629 better test fixes. --props=... instead of ...	commit \| commitdiff \| tree
2023-02-24	Ben Soares	JAL-629 Made ArgValuesMap helper class, simplifies...	commit \| commitdiff \| tree
2023-02-23	Ben Soares	JAL-629 test fixing	commit \| commitdiff \| tree
2023-02-23	Ben Soares	JAL-629 Add debug messages for more failing tests	commit \| commitdiff \| tree
2023-02-23	Ben Soares	JAL-629 fixed a Log4j test by adding --debug arg	commit \| commitdiff \| tree
2023-02-23	Ben Soares	JAL-629 bootstrap args and properties. Remember index...	commit \| commitdiff \| tree
2023-02-23	Ben Soares	JAL-629 nf-core sample alignment files and a2m versions	commit \| commitdiff \| tree
2023-02-23	Ben Soares	JAL-629 fix a PAEMatrix casting error	commit \| commitdiff \| tree
2023-02-22	Ben Soares	Merge branch 'develop' into features/r2_11_2_alphafold...	commit \| commitdiff \| tree
2023-02-22	Ben Soares	JAL-4064 JAL-4054 Corrected the tgz top-level dir from...	commit \| commitdiff \| tree
2023-02-22	Ben Soares	Merge branch 'develop' into features/r2_11_2_alphafold...	commit \| commitdiff \| tree
2023-02-21	Ben Soares	JAL-4088 Updated j8libs/*.jar in THIRDPARTYLIBS	commit \| commitdiff \| tree
2023-02-20	Ben Soares	JAL-3416 Turn off (partial) flatlaf scaling for HiDPI...	commit \| commitdiff \| tree
2023-02-20	Ben Soares	JAL-4064 JAL-4054 Correct names of mac arch installer...	commit \| commitdiff \| tree
2023-02-20	Ben Soares	Merge branch 'develop' into improvement/JAL-4111_suffixed_DE...	commit \| commitdiff \| tree
2023-02-20	Ben Soares	JAL-4128 Catch RasterFormatException caused whilst...	commit \| commitdiff \| tree
2023-02-20	Ben Soares	Merge branch 'develop' into bug/JAL-4125_flatlaf_quithandler...	commit \| commitdiff \| tree
2023-02-13	Ben Soares	Merge branch 'develop' into bug/JAL-4125_flatlaf_quithandler...	commit \| commitdiff \| tree
2023-02-13	Ben Soares	JAL-4125 Spanish translations	commit \| commitdiff \| tree
2023-02-13	Ben Soares	Merge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL...	commit \| commitdiff \| tree
2023-02-13	Ben Soares	JAL-4125 Move confirmation of closing external viewer...	commit \| commitdiff \| tree
2023-02-09	Ben Soares	JAL-4125 Additions to JvOptionPane and QuitHandler...	commit \| commitdiff \| tree
2023-02-03	Ben Soares	JAL-629 Fasta sequence id reading whitespace fix. Flexioble...	commit \| commitdiff \| tree
2023-02-03	Ben Soares	JAL-629 "updated" json-simple	commit \| commitdiff \| tree
2023-01-30	Ben Soares	JAL-1988 Make sensible choices if only the opening...	commit \| commitdiff \| tree
2023-01-26	Ben Soares	JAL-4118 remove unnecessary sleep from QuitHandlerTest	commit \| commitdiff \| tree
2023-01-26	Ben Soares	JAL-4118 fix a small buglet in BackupFiles exhibited...	commit \| commitdiff \| tree
2023-01-26	Ben Soares	JAL-1988 Add a sleep to file save test to give time...	commit \| commitdiff \| tree
2023-01-26	Ben Soares	JAL-629 example files from nf-core	commit \| commitdiff \| tree
2023-01-26	Ben Soares	JAL-629 helper eclipse CLI run	commit \| commitdiff \| tree
2023-01-26	Ben Soares	JAL-629 adjust arg type for tempfac-shading -- was...	commit \| commitdiff \| tree
2023-01-23	Ben Soares	JAL-629 Attempts to add PAE to structure. --headless...	commit \| commitdiff \| tree
2023-01-18	Ben Soares	JAL-629 make sequence id key 'seqid'	commit \| commitdiff \| tree
2023-01-17	Ben Soares	JAL-3416 No longer needed	commit \| commitdiff \| tree
2023-01-17	Ben Soares	Merge branch 'develop' into merge/JAL-1988_JAL-3772...	commit \| commitdiff \| tree
2023-01-16	Ben Soares	JAL-3416 More tweaking of FlatLaf. Problem with macOS...	commit \| commitdiff \| tree
2023-01-11	Ben Soares	JAL-1988 JAL-3772 Mark the _default_ STARTUP_FILE as...	commit \| commitdiff \| tree
2023-01-11	Ben Soares	JAL-629 added Alphafold cif, pdb and PAE json files...	commit \| commitdiff \| tree
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