Build and run tests under Java 11
Build: #705 was successful Changes by Gitlab User
JIRA issues
This page shows the JIRA issues that have been linked to this build. This includes issues specified in commit messages, labels or comments, as well as issues manually linked to this build.
| Type | Key | Summary | Status | Assignee | Fix versions | Related Builds | Operations |
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JAL-623 | pdb structure imported from paste to alignment not loaded into new Jmol window | Open | James Procter | 5 related builds | ||
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JAL-629 | create sequence/structure associations and add associated data via command line | Closed | Ben Soares | 2.11.3.0, 2.11.3, 2.11.5.0 | 7 related builds | |
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JAL-2275 | Cannot view local structures imported via direct network mount (e.g. cifs/samba, onedrive, etc) | Ready for testing | James Procter | 2.11.5.0, 2.12.0, 2.11.5.1 | 6 related builds | |
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JAL-2690 | No structure mapping made for CIF file imported by drag'n'drop of URL link | Open | James Procter | 2.12.0, 2.11.5.2 | 5 related builds | |
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JAL-3726 | Sequence ID colourscheme is not applied when view restored from project | Closed | James Procter | 2.11.2, 2.11.5.0 | 5 related builds | |
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JAL-3880 | show additional metadata along side annotation row labels | In Progress | James Procter | 2.11.5.0, 2.12.0 | 5 related builds | |
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JAL-3914 | Import model reliability scores encoded as temperature factor annotation with their correct name and semantics | Closed | James Procter | 2.11.5.0, 2.11.4, 2.11.5, 2.12.0 | 5 related builds | |
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JAL-3921 | structure view saved in project file as zero length entry - project load doesn't open viewer correctly | Closed | James Procter | 2.11.2.0, 2.11.3.0, 2.11.5.0 | 6 related builds | |
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JAL-3987 | Consensus secondary structure annotation rows for sequences with multiple sources of structural data | Closed | Renia Correya | 2.11.5.0 | 5 related builds | |
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JAL-4077 | Saving a project with a Jmol view on windows doesn't restore Jmol views | Ready for testing | Unassigned | 2.11.5.0, 2.12.0, 2.11.5.1 | 6 related builds | |
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JAL-4333 | error while using 'Calculate > Translate as cDNA' | Closed | James Procter | 2.11.5.0 | 5 related builds | |
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JAL-4334 | Uniprot parser does not support sequence features with 'unknown' start or end | Closed | James Procter | 2.11.3.0 | 5 related builds | |
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JAL-4350 | Easier to maintain autodiscovery of external structure viewers via exclusion list | Closed | Ben Soares | 2.11.5.0 | 5 related builds | |
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JAL-4386 | Calculate tree using secondary structure annotation | Closed | Renia Correya | 2.11.4.0, 2.11.5.0 | 5 related builds | |
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JAL-4392 | Consensus secondary structure visualization for alignments | Closed | Renia Correya | 2.11.4.0, 2.11.5.0 | 5 related builds | |
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JAL-4397 | 8 tests are failing on linux that aren't on macOS and 1 test failing on both | Closed | Ben Soares | 2.11.4.0, 2.11.5.0 | 5 related builds | |
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JAL-4399 | Consensus annotations and Tree visualisations for sequence annotation | Open | Renia Correya | 2.11.5.0, 2.11.4, 2.12.0 | 5 related builds | |
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JAL-4411 | Record source metadata in 3D structure data derived/transferred annotation rows | Closed | Renia Correya | 2.11.4.0, 2.11.5.0 | 6 related builds | |
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JAL-4426 | Show number of sequences contributing to the consensus secondary structure in the status bar/tool tip | Closed | James Procter | 2.11.5.0 | 5 related builds | |
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JAL-4428 | integrate OSX codesigning scripts in jalview's repository | Closed | James Procter | 2.11.4.0, 2.11.5.0 | 5 related builds | |
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JAL-4435 | Label sequence groups and shade tree internal nodes with diversity information | Closed | Renia Correya | 2.11.5.0 | 5 related builds | |
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JAL-4436 | Colour by secondary structure conservation | Closed | Renia Correya | 2.11.5.0 | 5 related builds | |
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JAL-4440 | Jmol view doesn't show all selected structures in 3d structure chooser mapped to sequences | In Progress | James Procter | 2.12.0 | 5 related builds | |
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JAL-4441 | optionally display source/provider for structure derived annotations along side the annotation label | Closed | James Procter | 2.11.5.0 | 5 related builds | |
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JAL-4454 | Automatically manage 'experimental' feature documentation in release notes | Reopened | James Procter | 2.11.4.0, 2.11.5.0, 2.12.0 | 5 related builds | |
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JAL-4469 | Uniprot Sequence Fetcher dialog allows version numbers to be excluded when given a list of versioned Uniprot/KB accessions | Closed | Ben Soares | 2.11.5.0 | 5 related builds | |
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JAL-4474 | jalview command doesn't work on Windows when user has a Network homedir | Being tested | James Procter | 2.11.5.0 | 5 related builds | |
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JAL-4477 | Jalview 2.11.4 installer doesn't work for usernames that include non-latin characters | Closed | Ben Soares | 2.11.5.0 | 5 related builds | |
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JAL-4482 | Gradle linkCheck task fails when whatsNew.html is not generated in non-CHANNEL builds | Closed | Ben Soares | 2.11.5.0 | 5 related builds | |
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JAL-4485 | Newer ChimeraX not found automatically on Windows or macOS desktops | Closed | Ben Soares | 2.11.5.0 | 5 related builds | |
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JAL-4486 | secondary structure annotation not mapped correctly to sequence for some structures | Open | Unassigned | 2.12, 2.11.5 | 5 related builds | |
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JAL-4487 | On Windows CLI, globbed input filenames with file separators might fail | Closed | Ben Soares | 2.11.5.0 | 5 related builds | |
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JAL-4491 | Could not obtain issue details from JIRA | |||||
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JAL-4500 | Update flatlaf for more OS visual integration | Closed | Ben Soares | 2.11.5.0 | 5 related builds | |
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JAL-4503 | Location of structure viewer not faithfully saved and restored in project | Closed | James Procter | 2.11.5.0, 2.12.0 | 6 related builds | |
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JAL-4504 | Jalview does not update the screen leading to the app becoming completely unusable | Closed | Ben Soares | 2.11.5.0 | 5 related builds | |
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JAL-4505 | install4j installation wizard looks bad in dark mode | Closed | Ben Soares | 2.11.5.0 | 5 related builds | |
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JAL-4507 | Exported Consensus annotation then loads (Load Features/Annotations) as a Pfam file sequence onto the alignment | Closed | Ben Soares | 2.11.5.0 | 5 related builds | |
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JAL-4509 | Assign perceptually distinct colours for secondary structure providers | Closed | Renia Correya | 2.11.5.0 | 5 related builds | |
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JAL-4511 | Jalview 2.11.4.1 doesn't include full platform details in console output | Closed | Ben Soares | 2.11.5.0 | 5 related builds | |
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JAL-4513 | Consistent colours assigned to groups generated when subdividing tree | Closed | Renia Correya | 2.11.5.0 | 5 related builds | |
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JAL-4515 | Add Coloured Backgrounds for Grouped Nodes in Similarity Tree | Closed | Renia Correya | 2.11.5.0 | 5 related builds | |
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JAL-4516 | Resizing an alignment window from the top can completely obscure sequences and annotation divider | Open | Unassigned | 5 related builds | ||
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JAL-4517 | store and restore trees linked to annotation rows in Jalview projects | Closed | Renia Correya | 2.11.5.0 | 7 related builds | |
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JAL-4518 | sort and colour annotation rows in alignment view according to tree ordering | Closed | Renia Correya | 2.11.5.0 | 5 related builds | |
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JAL-4527 | Allow secondary structure rows with 'PROVIDER' metadata to be exported and imported as Jalview annotations file | Closed | Renia Correya | 2.11.5.0 | 5 related builds | |
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JAL-4528 | Allow calculation of annotation track based trees involving just one or two sequences | Closed | Renia Correya | 2.11.5.0 | 5 related builds | |
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JAL-4530 | Add an Applescript .app to the DMG to allow easy installation to ~/Applications folder and optionally add Jalview to the Dock | Closed | Ben Soares | 2.11.5.0 | 5 related builds | |
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JAL-4531 | Release 2.11.5.0 | Open | James Procter | 2.11.5.0 | 6 related builds | |
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JAL-4537 | Tree node labels are grey when a tree is first created then black when redrawn | Closed | Renia Correya | 2.11.5.0 | 5 related builds | |
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JAL-4539 | find causes stack overflow | Closed | Renia Correya | 2.11.5.1 | 5 related builds | |
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JAL-4541 | Slight increase in robustness of analytics from Jalview Desktop | Being tested | James Procter | 2.11.5.0, 2.11.5 | 5 related builds | |
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JAL-4542 | Selection of Sequences in Sequence Panel should Highlight all Corresponding Nodes in Secondary Structure Similarity Tree and select annotations in annotation panel | Closed | Renia Correya | 2.11.5.0 | 6 related builds | |
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JAL-4548 | showing PDB IDs and other important metadata for annotations in the alignment and tree views | Closed | Renia Correya | 2.11.5.0 | 5 related builds | |
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JAL-4549 | trackpad scrolling on annotation panel when structure view is open causes massive slow down | Open | James Procter | 2.12.0 | 5 related builds | |
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JAL-4555 | Sort by a sequence's description | Closed | James Procter | 2.11.5.0 | 5 related builds | |
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JAL-4557 | New views for a CDS/Protein alignment have a 'cDNA PID' annotation row | Closed | James Procter | 2.11.5.0, 2.12.0 | 5 related builds | |
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JAL-4562 | CLI ignores additional annotation files specified via --annotations | Closed | Ben Soares | 2.11.5.0 | 5 related builds | |
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JAL-4563 | cannot import structure via URL on command line | Closed | James Procter | 2.11.5.0 | 5 related builds | |
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JAL-4564 | Can't specify URLs via --open= | Closed | James Procter | 2.11.5.0 | 5 related builds | |
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JAL-4566 | Jalview can fail to properly import and map a structure to a sequence via its N&W aligner | Closed | James Procter | 2.11.5.0 | 5 related builds | |
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JAL-4568 | Jalview freezes when trying to export PNG or EPS from Jmol via the File->Export menu | Closed | James Procter | 2.11.5.0 | 5 related builds | |
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JAL-4570 | PAE tree always shown above the alignment view | Closed | James Procter | 2.11.5.0 | 5 related builds | |
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JAL-4583 | Incorrect sequence count in source specific secondary structure consensus | Closed | James Procter | 2.11.5.0 | 5 related builds | |
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JAL-4589 | Empty row in annotation panel shown when alignment first imported | Closed | James Procter | 2.11.5.0 | 5 related builds | |
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JAL-4590 | String.isBlank() not available under Java 8 | Closed | James Procter | 2.11.5.0 | 5 related builds | |
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JAL-4591 | Web URLs that do not provide content or encoding headers are not readable | Closed | James Procter | 2.11.5.0 | 5 related builds | |
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JAL-4594 | Secondary structure consensus appears to overlap with other annotation | Resolved | James Procter | 2.11.5.0, 2.12.0, 2.11.5.1 | 8 related builds | |
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JAL-4595 | option to show or hide all 'temperature factor' like annotation tracks | Open | James Procter | 5 related builds |