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JAL-4581
Secondary Structure Provider Colours for 2.11.5.1 - JalviewJS
Use GA4 / Plausible for jalview's online help documentationJAL-4577
structures with no biopolymer chains generate (non-fatal) exceptions when mapping them to a sequence
double clicking an internal node of a secondary structure tree to select lots of tracks seems to take a very long time
Jalview freezes when trying to display all alphafill structures for example alignmentJAL-4567
Improve dialog when attempting to open non-existing file
Out of date command line argument style used in the JVL docs
Enable column selection on line graph annotations
find causes stack overflow
allow trees/PCA for secondary structures when just one sequence is shown in alignment
Resizing an alignment window from the top can completely obscure sequences and annotation divider
Residue highlighting in pymol not working in 3.0.4
View selection menu under the Jmol views for superimposition not shown
FAQ for the 'delete userland getdown directory' to rescue a stubbornly broken Jalview install
Migrate to Java 11 for Jalview production versionJAL-4488
routine service and program integration tests
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
Dynamic value colouring of annotations, e.g. linegraph, can be misleading
Annotation not redrawn correctly when scrolling left-right via trackpad in wrap mode
Quitting the JalviewJS desktop makes the browser hang
spurious output image .extensions cause jalview CLI execution to fail with Null Pointer Exception
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 projectJAL-4219
Parse RNA secondary structure annotation from 'extended' fasta-style files
Annotation colouring dialog box doesn't remember 'use original colours' settings when opened via the Colour menu
Saving a project with a Jmol view on windows doesn't restore Jmol views
3D Beacons results in structure chooser don't include models if one of the selected sequences does not have a uniprot accession
Mouseover on genomic loci propagated to 2D and 3D structures of transcripts and products
CMD+click to toggling selection of column
New FAQ for opening the 'System java console'
Protein structure derived annotation tracks not automatically shown when 'add to alignment' preference is enabled (and not available unless it *is* ticked!)
No structure mapping made for CIF file imported by drag'n'drop of URL link
Cannot view local structures imported via direct network mount (e.g. cifs/samba, onedrive, etc)
Use PDBe numbering for sequences extracted from PDB files
Rectangular selection in PCA and PaSiMap
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