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JAL-4059 Converting Pattern/Matcher methods that are possibly incompatible with JS...
[jalview.git]
/
src
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jalview
/
io
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2023-10-19
Ben Soares
JAL-4305 Isolate and unify the Jalview object from...
tree
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commitdiff
2023-10-12
Ben Soares
JAL-3772 Fix the logic of prompt to save URL loaded...
tree
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commitdiff
2023-10-11
Ben Soares
JAL-3772 Preference to NOT prompt to save remotely...
tree
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commitdiff
2023-09-08
Ben Soares
JAL-4262 Dialog for GUI and WARN for CLI of old style...
tree
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commitdiff
2023-09-07
James Procter
JAL-4279 suppress error dialogs raised by file loader...
improvement/JAL-4279_gracefully_handle_failure_to_openviaCLI
tree
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commitdiff
2023-08-18
Ben Soares
Merge branch 'improvement/JAL-4206_improve_JalviewFileC...
tree
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commitdiff
2023-08-10
Ben Soares
JAL-629 Change all stdout and stderr output to use...
tree
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commitdiff
2023-07-12
James Procter
JAL-4223 - test and patch to ensure numbering matches...
tree
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commitdiff
2023-06-15
Ben Soares
JAL-4206 Use All Known Alignment Files as default until...
tree
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commitdiff
2023-06-14
Ben Soares
JAL-4026 if relative path in recently opened exists...
tree
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commitdiff
2023-06-14
Ben Soares
JAL-4206 unified dimensions
tree
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commitdiff
2023-06-14
Ben Soares
JAL-4206 Added recentlyOpenedCellRenderer to better...
tree
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commitdiff
2023-06-07
James Procter
JAL-4195 catch thrown exceptions (if any) during image...
tree
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commitdiff
2023-05-26
James Procter
Merge branch 'develop' into features/JAL-4134_use_annot...
tree
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commitdiff
2023-05-25
Ben Soares
JAL-4186 Turn JvOptionPane Callable<Void> handlers...
tree
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commitdiff
2023-05-22
James Procter
JAL-1551 spotless
tree
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commitdiff
2023-05-19
James Procter
Merge branch 'develop' into features/JAL-4134_use_annot...
tree
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commitdiff
2023-05-19
James Procter
JAL-1551 spotlessApply
tree
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commitdiff
2023-05-19
James Procter
JAL-1551 spotlessApply
tree
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commitdiff
2023-05-18
James Procter
JAL-4134 properly specify BinaryNode as a typed generic...
tree
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commitdiff
2023-05-17
Ben Soares
JAL-629 Tidy up tests and replaced methods before merge...
tree
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commitdiff
2023-05-17
Ben Soares
Merge branch 'develop' into features/r2_11_2_alphafold...
tree
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commitdiff
2023-05-17
James Procter
JAL-4184 export description line in stockholm
patch/JAL-4184_description_stockholm
tree
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commitdiff
2023-05-11
Ben Soares
JAL-629 Fix --tempfac. Hide non-working --notempfac...
tree
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commitdiff
2023-05-04
Ben Soares
JAL-629 More NG arguments: --features, --annotations...
tree
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commitdiff
2023-05-03
Ben Soares
JAL-629 added eps and imagemap. Added --output and...
tree
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commitdiff
2023-05-02
Ben Soares
JAL-629 Add --renderer arg/subval for vector output...
tree
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commitdiff
2023-04-19
Ben Soares
JAL-629 Now showing temp fac and secondary structure...
tree
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commitdiff
2023-04-12
Ben Soares
Merge branch 'develop' into features/r2_11_2_alphafold...
tree
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commitdiff
2023-03-24
James Procter
JAL-4158 first attempt at stashing colours for contact...
tree
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commitdiff
2023-03-24
Ben Soares
JAL-629 Test tidyup
tree
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commitdiff
2023-03-23
Ben Soares
JAL-629 refactor ArgParser and helper classes all to...
tree
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commitdiff
2023-03-17
Ben Soares
JAL-629 All applications System.exits going through...
tree
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commitdiff
2023-03-15
Ben Soares
JAL-629 Commands more objecty, less classy. FileLoader...
tree
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commitdiff
2023-03-08
James Procter
Merge branch 'features/r2_11_2_alphafold/JAL-629' into...
tree
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commitdiff
2023-03-02
Ben Soares
JAL-629 Removal of unnecessary methods. Set pLTTD tempf...
tree
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commitdiff
2023-03-02
Ben Soares
JAL-629 Some refactoring to allow more flexible use...
tree
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commitdiff
2023-02-27
James Procter
Merge branch 'develop' into features/JAL-4134_treeviewe...
tree
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commitdiff
2023-02-24
James Procter
Merge branch 'features/r2_11_2_alphafold/JAL-629' into...
features/JAL-3858_PAEsInProjects
tree
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commitdiff
2023-02-23
James Procter
JAL-4134 - brutal hack to build a tree clustering colum...
tree
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commitdiff
2023-02-23
James Procter
JAL-4134 - refactor tree calculation code to work with...
tree
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commitdiff
2023-02-22
James Procter
JAL-3858 persist PAE matrix (only so far) as serialised...
tree
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commitdiff
2023-02-22
Ben Soares
Merge branch 'develop' into features/r2_11_2_alphafold...
tree
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commitdiff
2023-02-22
James Procter
JAL-4027 JAL-3858 rename CUSTOM_RENDERER to CONTACT_MAT...
tree
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commitdiff
2023-02-20
Ben Soares
Merge branch 'develop' into bug/JAL-4125_flatlaf_quitha...
bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_properly
tree
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commitdiff
2023-02-16
James Procter
Merge branch 'features/r2_11_2_alphafold/JAL-629' into...
tree
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commitdiff
2023-02-13
Ben Soares
Merge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL...
tree
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commitdiff
2023-02-13
James Procter
Merge branch 'develop' into feature/JAL-1713_overviewIn...
tree
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commitdiff
2023-02-03
Ben Soares
JAL-629 Fasta sequence id reading whitespace fix. Flexi...
tree
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commitdiff
2023-02-03
James Procter
Merge branch 'develop' into features/r2_11_2_alphafold...
tree
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commitdiff
2023-01-31
James Procter
JAL-1713 update from Jalview 2.11.3 develop
tree
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commitdiff
2023-01-30
Ben Soares
JAL-1988 Make sensible choices if only the opening...
merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
tree
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commitdiff
2023-01-26
Ben Soares
JAL-4118 fix a small buglet in BackupFiles exhibited...
tree
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commitdiff
2023-01-24
James Procter
JAL-629 need to delay call to AlignFile.parse() if...
tree
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commitdiff
2023-01-23
Ben Soares
JAL-629 Attempts to add PAE to structure. --headless...
tree
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commitdiff
2023-01-11
Ben Soares
JAL-629 refactoring TFType. Remove i18n identification...
tree
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commitdiff
2022-12-05
Ben Soares
JAL-629 implementation of --tempfac options
tree
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commitdiff
2022-11-09
Ben Soares
Merge branch 'improvement/JAL-3416_default_to_LIVE_DRAG...
tree
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commitdiff
2022-11-09
Ben Soares
JAL-3416 Add necessary logo to non-internal Frames
tree
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commitdiff
2022-11-09
Ben Soares
Merge branch 'improvement/JAL-3416_default_to_LIVE_DRAG...
tree
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commitdiff
2022-11-09
Ben Soares
JAL-3416 Remove all JFrame/JInternalFrame icons (set...
tree
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commitdiff
2022-11-04
Ben Soares
JAL-1998 JAL-3772 JAL-3416 Merge conflict resolution...
tree
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commitdiff
2022-11-03
Ben Soares
JAL-3416 File Chooser iconified, JvOptionPanes iconifie...
tree
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commitdiff
2022-11-01
Ben Soares
JAL-1988 JAL-3772 Change default alignmentviewport...
tree
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commitdiff
2022-10-27
Ben Soares
JAL-1988 Allow generic Container object in JvOptionPane...
tree
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commitdiff
2022-10-27
Ben Soares
Merge branch 'develop' into bug/JAL-1988_JAL-3772_impro...
tree
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commitdiff
2022-10-24
Ben Soares
JAL-1988 JAL-3772 wait timer working first time but...
tree
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commitdiff
2022-10-24
Ben Soares
JAL-1988 JAL-3772 Non-blocking modal dialogs for unsave...
tree
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commitdiff
2022-10-14
Jim Procter
Merge branch 'features/JAL-3895_alphafoldcolours' into...
tree
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commitdiff
2022-10-06
Jim Procter
JAL-1551 formatting
tree
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commitdiff
2022-10-06
Jim Procter
Patch for JAL-4074 - any content ending in ‘gzip’ recog...
tree
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commitdiff
2022-09-02
Ben Soares
JAL-1988 Added a saves in progress check for quit
tree
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commitdiff
2022-08-31
Ben Soares
JAL-1988 added a saveInProgress stack to BackupFiles
tree
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commitdiff
2022-06-10
Jim Procter
Merge branch 'features/r2_11_2_alphafold/JAL-2349_JAL...
tree
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commitdiff
2022-06-06
Jim Procter
JAL-4023 store distances as doubles
tree
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commitdiff
2022-04-16
Jim Procter
JAL-3365 expand range of allowed DSSP secondary structu...
tree
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commitdiff
2022-04-05
Jim Procter
JAL-3981 patch tests and remove errant imports
tree
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commitdiff
2022-04-05
Jim Procter
JAL-3990 gradle spotlessApply
tree
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commitdiff
2022-03-25
Jim Procter
JAL-3980 defensive copy - inefficient but fixes bug
tree
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commitdiff
2022-03-25
Jim Procter
JAL-3981 Additional line breaks - sort of helps
tree
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commitdiff
2022-03-24
Jim Procter
JAL-3981 strategic newlines to help speed up Java's...
tree
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commitdiff
2022-03-08
Jim Procter
JAL-3746 apply copyright to source
tree
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commitdiff
2022-03-08
Jim Procter
JAL-3438 spotless for 2.11.2.0
tree
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commitdiff
2022-03-08
Ben Soares
JAL-3103 Put jalview.jar first in getdown for .properti...
tree
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commitdiff
2022-02-16
Jim Procter
Merge branch 'develop' into features/r2_11_2_alphafold...
tree
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commitdiff
2022-02-11
Ben Soares
Merge branch 'update/JAL-3949_jalview_bin_Console_to_cu...
tree
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commitdiff
2022-02-11
Ben Soares
JLogger loglevel check on whether to call the actual...
tree
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commitdiff
2022-02-11
Jim Procter
JAL-3949 - refactor logging from jalview.bin.Cache...
tree
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commitdiff
2022-02-11
Ben Soares
Merge branch 'develop' into update/JAL-3949_abstracted_...
tree
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commitdiff
2022-02-11
Ben Soares
JAL-3949 Complete new abstracted logging framework...
tree
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commitdiff
2022-02-07
Jim Procter
Merge branch 'feature/JAL-1713_overviewInProject' into...
tree
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commitdiff
2022-02-07
Jim Procter
JAL-3785 JAL- Merge branch 'bug/JAL-3785autoOverviewTit...
bug/JAL-3785autoOverviewTitle
tree
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commitdiff
2022-02-04
Ben Soares
JAL-3949 An attempt at converting to Log4j 2 -- no...
tree
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commitdiff
2022-01-28
Jim Procter
Merge branch 'merge/develop_JAL-3725' into develop
tree
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commitdiff
2022-01-26
Jim Procter
JAL-3806 JAL-3725 propagate relaxed criteria for stop...
tree
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commitdiff
2022-01-26
gmungoc
JAL-3725 restrict mapped virtual feature location to...
tree
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commitdiff
2022-01-17
Ben Soares
JAL-3703 fix Gff3 shared InputStream with embedded...
tree
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commitdiff
2022-01-17
Ben Soares
close filehandles straight after parse, without setting...
tree
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commitdiff
2022-01-11
Ben Soares
JAL-3703 fix Gff3 shared InputStream with embedded...
tree
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commitdiff
2022-01-11
Ben Soares
close filehandles straight after parse, without setting...
tree
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commitdiff
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