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Commits : Listings

Analyzed over 1 year ago. based on code collected over 1 year ago.
Feb 13, 2023 — Feb 13, 2024
Commit Message Contributor Files Modified Lines Added Lines Removed Code Location Date
JAL-4279 move on if the file doesn't exist, or Identify fails for the file.
James Procter
More... over 1 year ago
JAL-4279 catch exceptions with fileLoader and report when we don’t get an alignment frame after trying to import a given file before moving on.
James Procter
More... over 1 year ago
JAL-629 Change names of Opt.ALLOWALL to Opt.ALLOWMULTIID and Opt.MULTI to Opt.MULTIVALUE. Remove filename value open* as trigger for applying an output file to all globbed files opened in the last --open, and make it the default option for globbed files opened. Adjust 2 test data for removed 'open*'.
Ben Soares
More... over 1 year ago
JAL-4090 JAL-4160 JAL-4274 image export dimensions and scale factor configurable via .jalview_properties as well as command line
James Procter
More... over 1 year ago
JAL-4273 release notes for visible adjuster marks, and patch so they are not rendered during figure export
James Procter
More... over 1 year ago
JAL-4090 report JAL-4261 known issue
James Procter
More... over 1 year ago
JAL-4260 attempt to rejig paging when id width is adjusted whilst in wrapped mode.
James Procter
More... over 1 year ago
JAL-4258 remove unnecessary ‘this’
James Procter
More... over 1 year ago
JAL-4259 construct a new SequenceRenderer when rendering an MSA to an exporter
James Procter
More... over 1 year ago
JAL-629 javadoc on new setMapping variant for structureselectionmanager
James Procter
More... over 1 year ago
JAL-629 reinstate INFO level stack trace from StructureChooser service exceptions and suppress external service queries when viewing structures via Command-line import
James Procter
More... over 1 year ago
JAL-629 javadoc
James Procter
More... over 1 year ago
JAL-629 remove structure viewer from the list of structure viewer base instances when its closeViewer method is called
James Procter
More... over 1 year ago
JAL-629 use JalviewStructureDisplayI in place of StructureViewerBase
James Procter
More... over 1 year ago
JAL-3088 check for validEnd when working out whether arrow should point to left when last base is paired
James Procter
More... over 1 year ago
JAL-4250 fix location and height for RNA secondary structure stem arrows
James Procter
More... over 1 year ago
JAL-4250 rendition is way too obscure for me
James Procter
More... over 1 year ago
Merge branch 'feature/JAL-629_--output_-_means_output_to_STDOUT' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Ben Soares
More... over 1 year ago
JAL-629 Add accessors for argParser and bootstrapArgs
Ben Soares
More... over 1 year ago
Merge branch 'feature/JAL-629_--output_-_means_output_to_STDOUT' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Ben Soares
More... over 1 year ago
JAL-629 Save structure frames in project files when opened and saved in headless mode
Ben Soares
More... over 1 year ago
Merge branch 'feature/JAL-629_--output_-_means_output_to_STDOUT' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Ben Soares
More... over 1 year ago
JAL-629 Fix --structureimage and options
Ben Soares
More... over 1 year ago
JAL-4124 need to repaint alignFrames imported from project after resolving references so PAE matrices are displayed
James Procter
More... over 1 year ago
JAL-4124 matrix is saved in dataset, with forward references made from alignments
James Procter
More... over 1 year ago
JAL-4124 add strategic newlines in matrix stringified representation so it doesn’t trigger buffer overflows for some parsers/editors
James Procter
More... over 1 year ago
Merge branch 'improvement/JAL-3830_remove_dock_icon_in_headless_mode' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Ben Soares
More... over 1 year ago
JAL-3830 Remove dock icon for -h too
Ben Soares
More... over 1 year ago
Merge branch 'features/r2_11_2_alphafold/JAL-629' into merge/big_merge_of_bens_stuff_before_2_11_3_0
Ben Soares
More... over 1 year ago
JAL-629 Small buglet with getting --seqid
Ben Soares
More... over 1 year ago