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JAL-4184 failing test for description export and re-import from stockholm
2023-03-08
Ben Soares
JAL-629 Fix --headless for new args. Fix progressbar...
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2023-03-08
Ben Soares
JAL-629 stash some TFType and PAEFile info into a PDBEntry
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2023-03-06
Ben Soares
JAL-629 Fix null AlignPanel. More descriptive label...
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2023-03-03
Ben Soares
JAL-629 Improved consistency of ArgParser classes ...
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2023-03-02
Ben Soares
JAL-629 slight tidy up
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2023-03-02
Ben Soares
JAL-629 Removal of unnecessary methods. Set pLTTD tempfac...
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2023-03-02
Ben Soares
JAL-629 Some refactoring to allow more flexible use...
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2023-02-28
Ben Soares
JAL-629 Firm up bootstrapArgs. Correct '-colour' in...
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2023-02-27
Ben Soares
JAL-629 add AF examples for FER1_SPIOL. Link and display...
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2023-02-27
Ben Soares
JAL-629 Fix Exceptions when running with CLI not headless
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2023-02-27
Ben Soares
JAL-629 Guesstimate whether to set pLDDT with PDB file
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2023-02-27
Ben Soares
JAL-629 JAL-4124 JAL-3855 remove deleted debugging...
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2023-02-27
Ben Soares
Merge branch 'develop' into features/r2_11_2_alphafold...
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2023-02-27
Ben Soares
JAL-629 removed debug prints. added .cif. added some...
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2023-02-26
Ben Soares
JAL-629 PAE matrix file guesstimate from filename
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2023-02-24
Ben Soares
JAL-629 Position GUI widgets for PDF file options....
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2023-02-24
Ben Soares
Merge branch 'develop' into features/r2_11_2_alphafold...
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2023-02-24
Ben Soares
JAL-629 add widgets to StructureChooser for tempfac...
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2023-02-24
Ben Soares
JAL-629 helper function for getting sensible structure...
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2023-02-24
Ben Soares
JAL-629 better test fixes. --props=... instead of ...
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2023-02-24
Ben Soares
JAL-629 Made ArgValuesMap helper class, simplifies...
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2023-02-23
Ben Soares
JAL-629 test fixing
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2023-02-23
Ben Soares
JAL-629 Add debug messages for more failing tests
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2023-02-23
Ben Soares
JAL-629 fixed a Log4j test by adding --debug arg
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2023-02-23
Ben Soares
JAL-629 bootstrap args and properties. Remember index...
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2023-02-23
Ben Soares
JAL-629 nf-core sample alignment files and a2m versions
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2023-02-23
Ben Soares
JAL-629 fix a PAEMatrix casting error
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2023-02-22
Ben Soares
Merge branch 'develop' into features/r2_11_2_alphafold...
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2023-02-22
Ben Soares
JAL-4064 JAL-4054 Corrected the tgz top-level dir from...
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2023-02-22
Ben Soares
Merge branch 'develop' into features/r2_11_2_alphafold...
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2023-02-21
Ben Soares
JAL-4088 Updated j8libs/*.jar in THIRDPARTYLIBS
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2023-02-20
Ben Soares
JAL-3416 Turn off (partial) flatlaf scaling for HiDPI...
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2023-02-20
Ben Soares
JAL-4064 JAL-4054 Correct names of mac arch installer...
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2023-02-20
Ben Soares
Merge branch 'develop' into improvement/JAL-4111_suffixed_DE...
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2023-02-20
Ben Soares
JAL-4128 Catch RasterFormatException caused whilst...
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2023-02-20
Ben Soares
Merge branch 'develop' into bug/JAL-4125_flatlaf_quithandler...
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2023-02-13
Ben Soares
Merge branch 'develop' into bug/JAL-4125_flatlaf_quithandler...
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2023-02-13
Ben Soares
JAL-4125 Spanish translations
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2023-02-13
Ben Soares
Merge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL...
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2023-02-13
Ben Soares
JAL-4125 Move confirmation of closing external viewer...
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2023-02-09
Ben Soares
JAL-4125 Additions to JvOptionPane and QuitHandler...
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2023-02-03
Ben Soares
JAL-629 Fasta sequence id reading whitespace fix. Flexioble...
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2023-02-03
Ben Soares
JAL-629 "updated" json-simple
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2023-01-30
Ben Soares
JAL-1988 Make sensible choices if only the opening...
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2023-01-26
Ben Soares
JAL-4118 remove unnecessary sleep from QuitHandlerTest
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2023-01-26
Ben Soares
JAL-4118 fix a small buglet in BackupFiles exhibited...
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2023-01-26
Ben Soares
JAL-1988 Add a sleep to file save test to give time...
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2023-01-26
Ben Soares
JAL-629 example files from nf-core
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2023-01-26
Ben Soares
JAL-629 helper eclipse CLI run
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2023-01-26
Ben Soares
JAL-629 adjust arg type for tempfac-shading -- was...
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2023-01-23
Ben Soares
JAL-629 Attempts to add PAE to structure. --headless...
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2023-01-18
Ben Soares
JAL-629 make sequence id key 'seqid'
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2023-01-17
Ben Soares
JAL-3416 No longer needed
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2023-01-17
Ben Soares
Merge branch 'develop' into merge/JAL-1988_JAL-3772...
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2023-01-16
Ben Soares
JAL-3416 More tweaking of FlatLaf. Problem with macOS...
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2023-01-11
Ben Soares
JAL-1988 JAL-3772 Mark the _default_ STARTUP_FILE as...
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2023-01-11
Ben Soares
JAL-629 added Alphafold cif, pdb and PAE json files...
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2023-01-11
Ben Soares
JAL-629 refactoring TFType. Remove i18n identification...
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2023-01-06
Ben Soares
JAL-3416 More explicit setting of FlatLaf macOS theme
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2023-01-06
Ben Soares
JAL-3416 Upgraded FlatLaf to 3.0 and added macOS theme...
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2023-01-06
Ben Soares
JAL-3416 remove a missed panel titlebar icon in TreePanel
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2023-01-06
Ben Soares
JAL-3416 Fix file permissions on bundled macOS JREs
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2023-01-06
Ben Soares
JAL-4111 Added commit and date text to splashscreens...
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2023-01-05
Ben Soares
JAL-4111 improvement to convert -draw argument
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2023-01-05
Ben Soares
JAL-4111 Use ImageMagick to add commit and build time...
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2023-01-05
Ben Soares
JAL-4111 Fixed channel.props to allow replacement of...
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2023-01-05
Benedict Soares...
JAL-4111 fixed DMG background image for generic Develop...
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2022-12-22
Ben Soares
JAL-4111 Allow -PCHANNEL=DEVELOP-version for new appbase...
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2022-12-19
Ben Soares
JAL-629 Add image output and quit
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2022-12-15
Ben Soares
JAL-629 move SubId to more logical place. Attempt removal...
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2022-12-14
Ben Soares
JAL-629 Open Structure Viewer from cmdline
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2022-12-09
Ben Soares
JAL-629 null check, fixed tests!
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2022-12-08
Ben Soares
JAL-629 fix opening files
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2022-12-08
Ben Soares
JAL-629 stray code deleted
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2022-12-08
Ben Soares
JAL-629 Allow attachment of pAE file to a particular...
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2022-12-05
Ben Soares
JAL-629 implementation of --tempfac options
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2022-11-30
Ben Soares
JAL-4101 Updated Rfam* tests
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2022-11-30
Ben Soares
JAL-4101 Updated DEFAULT_RFAM_BASEURL
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2022-11-29
Ben Soares
JAL-4101 Updated Rfam* tests
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2022-11-29
Ben Soares
JAL-4101 Updated DEFAULT_RFAM_BASEURL
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2022-11-23
Ben Soares
JAL-629 Doing things with the command line arguments
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2022-11-17
Ben Soares
JAL-4019 Clarification of position on 'X' in help text
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2022-11-16
Ben Soares
Merge branch 'improvement/JAL-3416_default_to_LIVE_DRAG_MODE...
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2022-11-16
Ben Soares
JAL-3416 make flatlaf default for linux
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2022-11-16
Ben Soares
JAL-4019 finalised a boolean option and tidied some...
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2022-11-14
Ben Soares
JAL-4019 Put original test back
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2022-11-14
Ben Soares
JAL-4019 Make diagnostic message debug level
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2022-11-13
Ben Soares
JAL-4019 small colour fix for X in the documentation
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2022-11-13
Ben Soares
JAL-4019 attribution to Suzanne
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2022-11-13
Ben Soares
JAL-4019 Help pages for Nucleotide Ambiguity colour...
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2022-11-13
Ben Soares
JAL-4019 small but important corrections to array order...
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2022-11-13
Ben Soares
JAL-4019 Added tests for new Nucleotide sequence detection
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2022-11-13
Ben Soares
JAL-4019 improvement to short sequence nucleotide detection...
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2022-11-10
Ben Soares
JAL-4019 Nucleotide Ambiguity Colour Scheme added....
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2022-11-09
Ben Soares
JAL-3416 Add necessary logo to non-internal Frames
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2022-11-09
Ben Soares
Merge branch 'improvement/JAL-3416_default_to_LIVE_DRAG_MODE...
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2022-11-09
Ben Soares
JAL-3416 Add necessary logo to non-internal Frames
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2022-11-09
Ben Soares
Merge branch 'improvement/JAL-3416_default_to_LIVE_DRAG_MODE...
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2022-11-09
Ben Soares
JAL-3416 Remove all JFrame/JInternalFrame icons (set...
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2022-11-09
Ben Soares
Merge branch 'bug/JAL-1988_JAL-3772_improved_quit_handling...
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