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JAL-4543
Enable column selection on line graph annotations
Selection of Sequences in Sequence Panel Does Not Highlight Corresponding Nodes in Secondary Structure Similarity TreeJAL-4540
Tree calculation out of memory error not passed to user!
find causes stack overflow
Select/Hide/Highlight columns or sequence positions by per-sequence annotation
Tree node labels incorrectly appear grey when a tree is first createdJAL-4531
Release 2.11.5.0
Add an Applescript .app to the DMG to allow easy installation to ~/Applications folder and optionally add Jalview to the Dock
Allow calculation of annotation track based trees involving just one or two sequences
Allow secondary structure rows with 'PROVIDER' metadata to be exported and imported as Jalview annotations file
Update jalview webservices documentation page
Loading progress bar remains visible indefinitely for some structures in SIMSApiper data
allow trees/PCA for secondary structures when just one sequence is shown in algiment
sensible precision for tree distance labels
store and restore trees linked to annotation rows in Jalview projects
Resizing an alignment window from the top can completely obscure sequences and annotation divider
Add Coloured Backgrounds for Grouped Nodes in Similarity Tree
Residue highlighting in pymol not working in 3.0.4
Consistent colours assigned to groups generated when subdividing tree
Assign perceptually distinct colours for secondary structure providers
Exported Consensus annotation then loads (Load Features/Annotations) as a Pfam file sequence onto the alignment
install4j installation wizard looks bad in dark mode
Update flatlaf for more OS visual integration
Migrate to Java 11 for Jalview production versionJAL-4489
automatic clustering of sequences using distance matricesJAL-4488
routine service and program integration tests
secondary structure annotation not mapped correctly to sequence for some structures
Temporarily configure 3d structure viewer via CLI for a jalview session
CAN'T INSTALL Jalview
Reformat Secondary Structure Consensus Annotation Labels
jalview --version or other command line output include misleading 'Version: TEST' information
allow pairwise alignment gap parameters to be adjusted
cannot store/restore group associated secondary structure consensus annotationsJAL-4463
Importing lots of sequences and structures example
An app for a particular getdown channel can't launch builds from other channels due to failed background image downloads
Colour by secondary structure conservation
Label sequence groups and tree internal nodes with diversity information
integrate OSX codesigning scripts in jalview's repository
Show number of sequences contributing to the consensus secondary structure in the status bar/tool tip
optionally hide consensus/annotations when no data is available
Add subtitle in PCA and Tree panel
Jalview could recognise .features, .annotations and .newick files belonging to an alignment file when all dragged-and-dropped onto it
Record source metadata in derived/transferred annotation rows
Calculate tree using secondary structure annotation
PAE partition not shown in the same place when tree is closed and reopened, or layout changed, and cluster colours lost loading back from jalview project
nf-core/proteinfold integration
Parse RNA secondary structure annotation from 'extended' fasta-style files
Consensus secondary structure annotation rows for sequences with multiple sources of structural data
HiDPI support in Windows
View number of sequences per subgroup in a separate window
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JAL","validSearcher":true,"isShown":true},"fixfor":{"name":"Fix Version","viewHtml":" <div class=\"searcherValue\">\n \n <label class=\"fieldLabel\" for=\"fieldfixfor\">Fix Version:</label><span id=\"fieldfixfor\" class=\"fieldValue\">\n \n 2.11.5.0 </span></div>\n","editHtml":"\n <div class=\"field-group aui-field-projectconstant\" >\n <label for=\"searcher-fixfor\">Fix Version</label>\n <select class=\"select js-default-checkboxmultiselect\" id=\"searcher-fixfor\" multiple=\"multiple\" name=\"fixfor\" size=\"2\" >\n <optgroup label=\"\">\n <option value=\"-1\" title=\"No Version\">No Version</option>\n <option value=\"-2\" title=\"Unreleased Versions\">Unreleased Versions</option>\n <option value=\"-3\" title=\"Released Versions\">Released Versions</option>\n </optgroup>\n <optgroup label=\"Unreleased Versions\">\n <option value=\"id:2.11.12\" title=\"2.11.12\">2.11.12</option>\n <option value=\"id:2.11.3\" title=\"2.11.3\">2.11.3</option>\n <option value=\"id:2.11.3.3b1\" 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