JIRA Issues

This page lists the JIRA issues that have been linked to builds related to this plan, ordered by last built. This includes issues specified in commit messages, labels or comments for builds, as well as issues manually linked to builds.

JIRA Issues (26 issues)
Key	Summary	Status	Assignee	Fix versions	Related Builds	Last Built
JAL-1551	Standard source code formatting and editing settings	In Progress	Mungo Carstairs		3 related builds	Last built: 9 months ago
JAL-1713	Overview window isn't saved in project file	Closed	Mungo Carstairs	2.11.3.0, 2.11.3	2 related builds	Last built: 9 months ago
JAL-1988	Can quit Jalview while 'save project' is in progress	Closed	Ben Soares	2.11.3.0	2 related builds	Last built: 9 months ago
JAL-1998	PDBfile parser fails with 'ArithmeticException' for some PDB entries	Closed	Tochukwu Charles N Ofoegbu	2.10.0	1 related build	Last built: 9 months ago
JAL-2349	Contact prediction visualisation	In Progress	James Procter	2.12	2 related builds	Last built: 9 months ago
JAL-2353	ignore sequence version numbers in IDs when resolving database references	Closed	James Procter	2.11.2, 2.11.2.6, 2.11.3.0, 2.11.3	2 related builds	Last built: 9 months ago
JAL-3077	Capture correct accession version when retrieving from Ensembl	In Progress	James Procter	2.11.1, 2.12.0	2 related builds	Last built: 9 months ago
JAL-3416	FlatLAF default look and feel on Linux, OSX and everywhere else ?	Closed	Ben Soares	2.11.2.6, 2.11.3.0	2 related builds	Last built: 9 months ago
JAL-3772	Prompt to save unsaved Alignment windows on close or quit	Closed	Ben Soares	2.11.3.0	4 related builds	Last built: 9 months ago
JAL-3776	Cancelling interactive calculation leaves empty progress bar.	Ready for testing	Mateusz Warowny	2.12.0	1 related build	Last built: 9 months ago
JAL-3855	Discover and import alphafold2 models and metadata from https://alphafold.ebi.ac.uk/	Closed	James Procter	2.11.3.0, 2.11.3	2 related builds	Last built: 9 months ago
JAL-4019	Ambiguous Base Colourscheme	Closed	Ben Soares	2.11.3.0	2 related builds	Last built: 9 months ago
JAL-4054	Review new features in install4j10 and install on build server	Closed	Ben Soares	2.11.3.0	2 related builds	Last built: 9 months ago
JAL-4064	Native M1 build for macOS using Adoptium JRE 11 macos-aarch64	Closed	Ben Soares	2.11.3.0, 2.11.3	2 related builds	Last built: 9 months ago
JAL-4090	Release 2.11.3.0	Closed	James Procter	2.11.3.0	5 related builds	Last built: 9 months ago
JAL-4095	interactive picking of regions in pAE matrices	Closed	James Procter	2.11.3.0	2 related builds	Last built: 9 months ago
JAL-4101	Rfam API domain has changed. Old domain certificate has expired.	Closed	Ben Soares	2.11.2.6	1 related build	Last built: 9 months ago
JAL-4102	2.11.2.6 patch release	Closed	James Procter	2.11.2.6	2 related builds	Last built: 9 months ago
JAL-4104	Application ownership	Open	Ben Soares	2.12.0, 2.12	2 related builds	Last built: 9 months ago
JAL-4114	Jalview 2.11.2.5 not compatible with 3d-beacons api v2.0	Closed	James Procter	2.11.2.6	2 related builds	Last built: 9 months ago
JAL-4116	PDB structures slow to view when Jalview Java console is open	Closed	James Procter	2.11.2.7, 2.11.3.0	2 related builds	Last built: 9 months ago
JAL-4118	Fix jalview.gui.QuitHandlerTest.testSavedProjectChanges and testSavedAlignmentChanges test failing on build server	Closed	Ben Soares	2.11.3.0	2 related builds	Last built: 9 months ago
JAL-4125	Flatlaf QuitHandler: Warning dialog about closing an external structure viewer doesn't display properly	Closed	Ben Soares	2.11.3.0	2 related builds	Last built: 9 months ago
JAL-4126	'use original colours' option of colour by annotation not honoured when restoring view from project	Closed	James Procter	2.11.3.0	2 related builds	Last built: 9 months ago
JAL-4127	'Reload' for a jalview project results in all windows being duplicated	Open	James Procter	2.12.0	2 related builds	Last built: 9 months ago