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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-3077 broken conflict resolve resulted in failing test (nb - still not resolved the issue of (promoted) dbrefs!)
James Procter
More... over 2 years ago
Fix for JAL-4126 - don’t automatically create a threshold line when no threshold line is needed when reconstructing the annotation colour scheme from a project file
James Procter
More... over 2 years ago
JAL-4126 comment out closeAll - so we can visually check the alignment frame as it is restored
James Procter
More... over 2 years ago
JAL-4126 failing test - colour scheme appears to be being created and configured, but the renderer is not actually using the colour scheme to shade the sequence when the project is restored.
James Procter
More... over 2 years ago
JAL-4125 Additions to JvOptionPane and QuitHandler with StructureViewerBase handling closed frame during quit differently. Still not working as dialog content does not appear until after quithandling thread has finished (it's blocking EDT). Need to break the doDesktopQuit Callable up into sections, that add another bit to the end when necessary.
Ben Soares
More... over 2 years ago
JAL-629 Fasta sequence id reading whitespace fix. Flexioble pae json keys and structure. Headless fixes. Logging fixes (MessageManager -- test broken). ArgParser and Console helper methods. Commands added e.g. --colour=gecos:flower.
Ben Soares
More... over 2 years ago
JAL-629 "updated" json-simple
Ben Soares
More... over 2 years ago
JAL-1551 remove temp file in src
James Procter
More... over 2 years ago
Merge branch 'develop' into features/r2_11_2_alphafold/JAL-2349_JAL-3855
James Procter
More... over 2 years ago
JAL-4119 JAL-2144 ‘invalid’ DBRefEntry has a null version field - never candidate for a primary sequence accession
James Procter
More... over 2 years ago
JAL-4119 use split_xml directories rather than the single path
James Procter
More... over 2 years ago
JAL-1713 update from Jalview 2.11.3 develop Merge branch 'develop' into feature/JAL-1713_overviewInProject regenerated jaxb classes to resolve conflicts
James Procter
More... over 2 years ago
JAL-1988 Make sensible choices if only the opening file has been opened, and alter the message if an alignment has been fetched but not changed
Ben Soares
More... over 2 years ago
JAL-4118 remove unnecessary sleep from QuitHandlerTest
Ben Soares
More... over 2 years ago
JAL-4118 fix a small buglet in BackupFiles exhibited in tests on build server. Possible problem with filename with dirs in passed to BackupFiles.
Ben Soares
More... over 2 years ago
JAL-1988 Add a sleep to file save test to give time for file to save
Ben Soares
More... over 2 years ago
JAL-629 example files from nf-core
Ben Soares
More... over 2 years ago
JAL-629 helper eclipse CLI run
Ben Soares
More... over 2 years ago
JAL-629 adjust arg type for tempfac-shading -- was grabbing next argument
Ben Soares
More... over 2 years ago
Merge branch 'patch/JAL-4116_slowtoopenstructure' into releases/Release_2_11_2_Branch
James Procter
More... over 2 years ago
JAL-4117 - version bump and release notes for JAL-4116
James Procter
More... over 2 years ago
JAL-4090 update from 2.11.2.7 JAL-4117 - version bump and release notes for JAL-4116
James Procter
More... over 2 years ago
JAL-4116 relegate the failed to promote warning to Console.debug so most users won’t even see it (or be slowed down by it).
James Procter
More... over 2 years ago
JAL-4116 relegate the failed to promote warning to Console.debug so most users won’t even see it (or be slowed down by it).
James Procter
More... over 2 years ago
Merge branch 'new_feature/JAL-4019_ambiguous_base_colourscheme' into develop
James Procter
More... over 2 years ago
JAL-4090 Release 2.11.3.0 release notes and version bump
James Procter
More... over 2 years ago
Merge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064' into develop
James Procter
More... over 2 years ago
JAL-629 hacked in --tempfac-shading - hardcoded to use existing colours in per-sequence annotation
James Procter
More... over 2 years ago
JAL-629 suggest not breaking out of the structure processing loop if just one structure has a bunk sequence association..
James Procter
More... over 2 years ago
JAL-629 need to delay call to AlignFile.parse() if StructureFile needs to configure itself at construction time
James Procter
More... over 2 years ago