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JAL-629 helper function for getting sensible structure (or other arg value)
2023-02-24 Ben SoaresJAL-629 helper function for getting sensible structure...
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2023-02-24 Ben SoaresJAL-629 better test fixes. --props=... instead of ...
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2023-02-24 Ben SoaresJAL-629 Made ArgValuesMap helper class, simplifies...
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2023-02-23 Ben SoaresJAL-629 test fixing
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2023-02-23 Ben SoaresJAL-629 Add debug messages for more failing tests
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2023-02-23 Ben SoaresJAL-629 fixed a Log4j test by adding --debug arg
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2023-02-23 Ben SoaresJAL-629 bootstrap args and properties. Remember index...
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2023-02-23 Ben SoaresJAL-629 nf-core sample alignment files and a2m versions
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2023-02-23 Ben SoaresJAL-629 fix a PAEMatrix casting error
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2023-02-22 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold...
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2023-02-22 Ben SoaresJAL-4064 JAL-4054 Corrected the tgz top-level dir from...
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2023-02-22 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold...
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2023-02-21 Ben SoaresJAL-4088 Updated j8libs/*.jar in THIRDPARTYLIBS
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2023-02-20 Ben SoaresJAL-3416 Turn off (partial) flatlaf scaling for HiDPI...
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2023-02-20 Ben SoaresJAL-4064 JAL-4054 Correct names of mac arch installer...
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2023-02-20 Ben SoaresMerge branch 'develop' into improvement/JAL-4111_suffixed_DE...
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2023-02-20 Ben SoaresJAL-4128 Catch RasterFormatException caused whilst...
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2023-02-20 Ben SoaresMerge branch 'develop' into bug/JAL-4125_flatlaf_quithandler...
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2023-02-13 Ben SoaresMerge branch 'develop' into bug/JAL-4125_flatlaf_quithandler...
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2023-02-13 Ben SoaresJAL-4125 Spanish translations
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2023-02-13 Ben SoaresMerge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL...
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2023-02-13 Ben SoaresJAL-4125 Move confirmation of closing external viewer...
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2023-02-09 Ben SoaresJAL-4125 Additions to JvOptionPane and QuitHandler...
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2023-02-03 Ben SoaresJAL-629 Fasta sequence id reading whitespace fix. Flexioble...
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2023-02-03 Ben SoaresJAL-629 "updated" json-simple
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2023-01-30 Ben SoaresJAL-1988 Make sensible choices if only the opening...
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2023-01-26 Ben SoaresJAL-4118 remove unnecessary sleep from QuitHandlerTest
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2023-01-26 Ben SoaresJAL-4118 fix a small buglet in BackupFiles exhibited...
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2023-01-26 Ben SoaresJAL-1988 Add a sleep to file save test to give time...
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2023-01-26 Ben SoaresJAL-629 example files from nf-core
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2023-01-26 Ben SoaresJAL-629 helper eclipse CLI run
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2023-01-26 Ben SoaresJAL-629 adjust arg type for tempfac-shading -- was...
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2023-01-23 Ben SoaresJAL-629 Attempts to add PAE to structure. --headless...
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2023-01-18 Ben SoaresJAL-629 make sequence id key 'seqid'
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2023-01-17 Ben SoaresJAL-3416 No longer needed
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2023-01-17 Ben SoaresMerge branch 'develop' into merge/JAL-1988_JAL-3772...
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2023-01-16 Ben SoaresJAL-3416 More tweaking of FlatLaf. Problem with macOS...
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2023-01-11 Ben SoaresJAL-1988 JAL-3772 Mark the _default_ STARTUP_FILE as...
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2023-01-11 Ben SoaresJAL-629 added Alphafold cif, pdb and PAE json files...
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2023-01-11 Ben SoaresJAL-629 refactoring TFType. Remove i18n identification...
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2023-01-06 Ben SoaresJAL-3416 More explicit setting of FlatLaf macOS theme
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2023-01-06 Ben SoaresJAL-3416 Upgraded FlatLaf to 3.0 and added macOS theme...
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2023-01-06 Ben SoaresJAL-3416 remove a missed panel titlebar icon in TreePanel
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2023-01-06 Ben SoaresJAL-3416 Fix file permissions on bundled macOS JREs
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2023-01-06 Ben SoaresJAL-4111 Added commit and date text to splashscreens...
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2023-01-05 Ben SoaresJAL-4111 improvement to convert -draw argument
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2023-01-05 Ben SoaresJAL-4111 Use ImageMagick to add commit and build time...
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2023-01-05 Ben SoaresJAL-4111 Fixed channel.props to allow replacement of...
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2022-12-22 Ben SoaresJAL-4111 Allow -PCHANNEL=DEVELOP-version for new appbase...
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2022-12-19 Ben SoaresJAL-629 Add image output and quit
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2022-12-15 Ben SoaresJAL-629 move SubId to more logical place. Attempt removal...
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2022-12-14 Ben SoaresJAL-629 Open Structure Viewer from cmdline
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2022-12-09 Ben SoaresJAL-629 null check, fixed tests!
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2022-12-08 Ben SoaresJAL-629 fix opening files
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2022-12-08 Ben SoaresJAL-629 stray code deleted
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2022-12-08 Ben SoaresJAL-629 Allow attachment of pAE file to a particular...
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2022-12-05 Ben SoaresJAL-629 implementation of --tempfac options
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2022-11-29 Ben SoaresJAL-4101 Updated Rfam* tests
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2022-11-29 Ben SoaresJAL-4101 Updated DEFAULT_RFAM_BASEURL
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2022-11-23 Ben SoaresJAL-629 Doing things with the command line arguments
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2022-11-17 Ben SoaresJAL-4019 Clarification of position on 'X' in help text
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2022-11-16 Ben SoaresMerge branch 'improvement/JAL-3416_default_to_LIVE_DRAG_MODE...
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2022-11-16 Ben SoaresJAL-3416 make flatlaf default for linux
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2022-11-16 Ben SoaresJAL-4019 finalised a boolean option and tidied some...
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2022-11-14 Ben SoaresJAL-4019 Put original test back
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2022-11-14 Ben SoaresJAL-4019 Make diagnostic message debug level
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2022-11-13 Ben SoaresJAL-4019 small colour fix for X in the documentation
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2022-11-13 Ben SoaresJAL-4019 attribution to Suzanne
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2022-11-13 Ben SoaresJAL-4019 Help pages for Nucleotide Ambiguity colour...
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2022-11-13 Ben SoaresJAL-4019 small but important corrections to array order...
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2022-11-13 Ben SoaresJAL-4019 Added tests for new Nucleotide sequence detection
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2022-11-13 Ben SoaresJAL-4019 improvement to short sequence nucleotide detection...
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2022-11-10 Ben SoaresJAL-4019 Nucleotide Ambiguity Colour Scheme added....
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2022-11-09 Ben SoaresJAL-3416 Add necessary logo to non-internal Frames
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2022-11-09 Ben SoaresMerge branch 'improvement/JAL-3416_default_to_LIVE_DRAG_MODE...
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2022-11-09 Ben SoaresJAL-3416 Add necessary logo to non-internal Frames
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2022-11-09 Ben SoaresMerge branch 'improvement/JAL-3416_default_to_LIVE_DRAG_MODE...
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2022-11-09 Ben SoaresJAL-3416 Remove all JFrame/JInternalFrame icons (set...
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2022-11-09 Ben SoaresMerge branch 'bug/JAL-1988_JAL-3772_improved_quit_handling...
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2022-11-09 Ben SoaresJAL-1988 JAL-3772 Test for FORCE_QUIT whilst saving...
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2022-11-08 Ben SoaresMerge branch 'bug/JAL-1988_JAL-3772_improved_quit_handling...
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2022-11-08 Ben SoaresJAL-1988 JAL-3776 Formatting JvOptionPane
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2022-11-08 Ben SoaresJAL-1988 JAL-3772 Tests for various quitting scenarios
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2022-11-08 Ben SoaresJAL-1988 JAL-3772 Fixes highlighted by tests
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2022-11-04 Ben SoaresMerge branch 'merge/JAL-4054+JAL-4064' into ben-big...
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2022-11-04 Ben SoaresJAL-3416 Added logoIcon to quit (and potentially other...
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2022-11-04 Ben SoaresJAL-1998 JAL-3772 JAL-3416 Merge conflict resolution...
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2022-11-04 Ben SoaresJAL-4064 JAL-4054 Combined install4j10 template with...
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2022-11-04 Ben SoaresJAL-4054 Altered file association templates and generated...
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2022-11-03 Ben SoaresJAL-3416 File Chooser iconified, JvOptionPanes iconified...
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2022-11-03 Ben SoaresJAL-1988 JAL-3772 Allow other window closing dialogs...
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2022-11-03 Ben SoaresJAL-3416 More JInternalFrame icons
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2022-11-03 Ben SoaresJAL-1988 JAL-3772 Tidying of unspecified Callable declaratio...
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2022-11-03 Ben SoaresJAL-3416 Start to add JInternalFrame icons (to replace...
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2022-11-02 Ben SoaresJAL-1988 JAL-3772 Moving packages to somewhere more...
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2022-11-01 Ben SoaresJAL-3416 set flatlaf default drag mode to LIVE_DRAG_MODE
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2022-11-01 Ben SoaresJAL-1988 JAL-3772 Change default alignmentviewport...
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2022-11-01 Ben SoaresJAL-4064 tidying build.gradle
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2022-11-01 Ben SoaresJAL-4064 re-added bundled macOS JREs as Filesets, which...
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2022-11-01 Ben SoaresJAL-4064 Cleaned up file sets in install4j template...
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