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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
2023-01-11	Ben Soares	JAL-629 refactoring TFType. Remove i18n identification...	commit \| commitdiff \| tree
2023-01-06	Ben Soares	JAL-3416 More explicit setting of FlatLaf macOS theme	commit \| commitdiff \| tree
2023-01-06	Ben Soares	JAL-3416 Upgraded FlatLaf to 3.0 and added macOS theme...	commit \| commitdiff \| tree
2023-01-06	Ben Soares	JAL-3416 remove a missed panel titlebar icon in TreePanel	commit \| commitdiff \| tree
2023-01-06	Ben Soares	JAL-3416 Fix file permissions on bundled macOS JREs	commit \| commitdiff \| tree
2023-01-06	Ben Soares	JAL-4111 Added commit and date text to splashscreens...	commit \| commitdiff \| tree
2023-01-05	Ben Soares	JAL-4111 improvement to convert -draw argument	commit \| commitdiff \| tree
2023-01-05	Ben Soares	JAL-4111 Use ImageMagick to add commit and build time...	commit \| commitdiff \| tree
2023-01-05	Ben Soares	JAL-4111 Fixed channel.props to allow replacement of...	commit \| commitdiff \| tree
2022-12-22	Ben Soares	JAL-4111 Allow -PCHANNEL=DEVELOP-version for new appbase...	commit \| commitdiff \| tree
2022-12-19	Ben Soares	JAL-629 Add image output and quit	commit \| commitdiff \| tree
2022-12-15	Ben Soares	JAL-629 move SubId to more logical place. Attempt removal...	commit \| commitdiff \| tree
2022-12-14	Ben Soares	JAL-629 Open Structure Viewer from cmdline	commit \| commitdiff \| tree
2022-12-09	Ben Soares	JAL-629 null check, fixed tests!	commit \| commitdiff \| tree
2022-12-08	Ben Soares	JAL-629 fix opening files	commit \| commitdiff \| tree
2022-12-08	Ben Soares	JAL-629 stray code deleted	commit \| commitdiff \| tree
2022-12-08	Ben Soares	JAL-629 Allow attachment of pAE file to a particular...	commit \| commitdiff \| tree
2022-12-05	Ben Soares	JAL-629 implementation of --tempfac options	commit \| commitdiff \| tree
2022-11-29	Ben Soares	JAL-4101 Updated Rfam* tests	commit \| commitdiff \| tree
2022-11-29	Ben Soares	JAL-4101 Updated DEFAULT_RFAM_BASEURL	commit \| commitdiff \| tree
2022-11-23	Ben Soares	JAL-629 Doing things with the command line arguments	commit \| commitdiff \| tree
2022-11-17	Ben Soares	JAL-4019 Clarification of position on 'X' in help text	commit \| commitdiff \| tree
2022-11-16	Ben Soares	Merge branch 'improvement/JAL-3416_default_to_LIVE_DRAG_MODE...	commit \| commitdiff \| tree
2022-11-16	Ben Soares	JAL-3416 make flatlaf default for linux	commit \| commitdiff \| tree
2022-11-16	Ben Soares	JAL-4019 finalised a boolean option and tidied some...	commit \| commitdiff \| tree
2022-11-14	Ben Soares	JAL-4019 Put original test back	commit \| commitdiff \| tree
2022-11-14	Ben Soares	JAL-4019 Make diagnostic message debug level	commit \| commitdiff \| tree
2022-11-13	Ben Soares	JAL-4019 small colour fix for X in the documentation	commit \| commitdiff \| tree
2022-11-13	Ben Soares	JAL-4019 attribution to Suzanne	commit \| commitdiff \| tree
2022-11-13	Ben Soares	JAL-4019 Help pages for Nucleotide Ambiguity colour...	commit \| commitdiff \| tree
2022-11-13	Ben Soares	JAL-4019 small but important corrections to array order...	commit \| commitdiff \| tree
2022-11-13	Ben Soares	JAL-4019 Added tests for new Nucleotide sequence detection	commit \| commitdiff \| tree
2022-11-13	Ben Soares	JAL-4019 improvement to short sequence nucleotide detection...	commit \| commitdiff \| tree
2022-11-10	Ben Soares	JAL-4019 Nucleotide Ambiguity Colour Scheme added....	commit \| commitdiff \| tree
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