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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.
| Type | Key | Summary | Status | Assignee | Fix versions | Related Builds | Last Built |
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JAL-3063 | Migrate from Castor to JAXB to enable Jalview project import/export in Jalview-js | Reopened | Mungo Carstairs | 2.11.0 | 2 related builds | Last built: 1 month ago |
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JAL-3196 | Gradle build with install4j launchers | Closed | Ben Soares | 2.11.0 | 2 related builds | Last built: 1 month ago |
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JAL-3384 | Redirect stdout and stderr to file when launched from getdown | Ready for testing | Ben Soares | 2 related builds | Last built: 1 month ago | |
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JAL-3631 | Allow jalview auto-updates to download to and work from separate user-space directory | Closed | Ben Soares | 2.11.4.0 | 8 related builds | Last built: 1 month ago |
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JAL-3830 | Add a command-line wrapper script to macOS bundle, linux and Windows installations (bash, powershell and .bat wrappers) | Closed | Ben Soares | 2.11.2, 2.11.2.0, 2.11.2.2, 2.11.3.0 | 2 related builds | Last built: 1 month ago |
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JAL-3845 | Add error message when launched directly from Jalview Installer DMG volume | Ready for testing | Ben Soares | 2 related builds | Last built: 1 month ago | |
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JAL-3987 | Consensus secondary structure annotation rows for sequences with multiple sources of structural data | In Progress | Renia Correya | 2.11.5.0 | 2 related builds | Last built: 1 month ago |
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JAL-4072 | Could not obtain issue details from JIRA | Last built: 1 month ago | ||||
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JAL-4104 | Application ownership | Closed | Ben Soares | 2.11.4.0 | 4 related builds | Last built: 1 month ago |
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JAL-4159 | PaSiMap inclusion | Closed | Thomas Morell | 2.11.4.0 | 12 related builds | Last built: 1 month ago |
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JAL-4160 | New command line argument framework | Closed | Ben Soares | 2.11.3.0 | 2 related builds | Last built: 1 month ago |
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JAL-4257 | allow adjustment of gap opening and extension for built in nw alignment | Closed | James Procter | 2.11.4.0 | 2 related builds | Last built: 1 month ago |
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JAL-4358 | Getdown splash screen should disappear as soon as the Jalview Desktop is created/visible | Ready for testing | Ben Soares | 2.11.3_js | 2 related builds | Last built: 1 month ago |
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JAL-4386 | Calculate tree using secondary structure annotation | In Progress | James Procter | 2.11.4.0, 2.11.5.0 | 9 related builds | Last built: 1 month ago |
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JAL-4392 | Consensus secondary structure visualization for alignments | Closed | Renia Correya | 2.11.4.0 | 6 related builds | Last built: 1 month ago |
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JAL-4409 | Implement in Jalview (and getdown for JVL) the use of specific scheme names for different channels (e.g. jalviewd://) | Reopened | Ben Soares | 2.11.4.0 | 2 related builds | Last built: 1 month ago |
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JAL-4411 | Record source metadata in derived/transferred annotation rows | In Progress | Renia Correya | 2.11.4.0, 2.11.5.0 | 2 related builds | Last built: 1 month ago |
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JAL-4414 | HTTP errors are often interpreted to the user as a file format error - and FileNotFound errors are not propagated from Web or Local file import | In Progress | Unassigned | 2.11.4.0, 2.11.4.1 | 10 related builds | Last built: 1 month ago |
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JAL-4417 | jalview.bin.CommandsTest.headlessOrGuiImageOutputTest produces different images for --gui and --headless when using certain .jalview_properties | Closed | Ben Soares | 2.11.4.0 | 1 related build | Last built: 1 month ago |
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JAL-4418 | Jalview 2.11.4.0 release | Being documented | James Procter | 2.11.4.0 | 38 related builds | Last built: 1 month ago |
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JAL-4420 | Jalview could recognise .features, .annotations and .newick files belonging to an alignment file when all dragged-and-dropped onto it | In Progress | Ben Soares | 2.11.4.0, 2.11.5.0 | 9 related builds | Last built: 1 month ago |
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JAL-4421 | Release installer DMG does not display the background image | Ready for testing | Ben Soares | 2.11.4, 2.12 | 8 related builds | Last built: 1 month ago |
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JAL-4441 | optionally display source/provider for structure derived annotations along side the annotation label | Being documented | James Procter | 2 related builds | Last built: 1 month ago | |
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JAL-789 | allow the alignment parameters and score matrix to be set for a pairwise sequence alignment | Open | James Procter | 2.12.0 | 10 related builds | Last built: 1 month ago |
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JAL-4436 | Colour by secondary structure conservation | In Progress | Renia Correya | 2.11.5.0 | 5 related builds | Last built: 2 months ago |
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