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JAL-4626
EMBL-EBI AlphaFold PAEs are not being importedJAL-4617
Release 2.11.5.1
install4j Windows installer wizard in dark mode needs background colour adjustment
Jmol doesn't interpret path correctly on university managed Windows desktop
Jalview 2.11.5.0 not launching for second or subsequent times from 2.11.4.0 installation on Windows or Linux
Export images of alignments missing part of sequenceJAL-4602
Hide the 'All' secondary structure consensus annotation when just one type is available
Manual import of JPred annotation data does not trigger display of secondary structure consensus
Secondary structure consensus appears to overlap with other annotation
Use GA4 / Plausible for jalview's online help documentation
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 alignment
Out of date command line argument style used in the JVL docs
find causes stack overflow
allow trees/PCA for secondary structures when just one sequence is shown in alignment
Residue highlighting in pymol not working in 3.0.4
View selection menu under the Jmol views for superimposition not shown
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
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-4243
bio.tools record accompanying Jalview source code
Saving a project with a Jmol view on windows doesn't restore Jmol views
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!)
Cannot view local structures imported via direct network mount (e.g. cifs/samba, onedrive, etc)
support for 'insertion positions' in a3m files [ was a2m - in UCSC speak)
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