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- JAL-3971
Spanish help and link checks for 2.11.2 series - JAL-3959
ENA, Rfam and Pfam retrieval fails for JalviewJS 2.11.0(pre-release) - JAL-3953
Update java2script bindings for log4j2 for JalviewJS - JAL-3949
Standard out logging broken: messages only routing to stderr and appear as a raw template - JAL-3937
PFAM services have a new certificate that JRE cacerts does not cover - JAL-3933
Use of log4j and mitigation of critical alert "Apache Log4j 2 vulnerability (CVE-2021-44228)" - JAL-3930
Add customizedId of "JALVIEW" to the Jalview Launcher in install4j - JAL-3925
quick annotation of a structure via sequence features (that can be undone) - JAL-3922
Highlight region in alignment selected via Jmol - JAL-3915
remove defunct RNAView from Jalview - JAL-3895
Alphafold red/orange/yellow/green colourscheme for structures - JAL-3885
SequenceFetcher JComboBox displays "PFAM" instead of "PFAM (Seed)" - JAL-3884
Suppress XMLParsing Error exceptions when retrieving Uniprot database refs for sequences - JAL-3877
Parse LOCUS line of GenBank file to obtain possibly missing ACCESSION id (and other useful metadata) - JAL-3867
clarify and document behaviour of Jalview Develop and Jalview Test specific configuration files - JAL-3865
Provide combined view of PDBe and 3d-beacons metadata for discovered structures - JAL-3863
Identify canonical Uniprot accessions in protein sequence cross-references - JAL-3856
Support extended PDB ids - JAL-3850
SimpleHttpFileServer no longer available in gradle 7 - JAL-3843
Fix the instructions given when Jalview (Develop) app fails to update the JVM needed for a getdown channel - JAL-3841
New top-level README - JAL-3837
Add GPL licence info to Splash screen and about - JAL-3836
Jalview File Open dialog should have an "All alignment files" option by default to show all possible alignment files that can be opened - JAL-3832
spike '3d-beacons' sequence fetcher to get the FTSRestClient/GUI working - JAL-3830
Add a command-line wrapper script to macOS bundle, linux and Windows installations (bash, powershell and .bat wrappers) - JAL-3829
Jalview 3D-Beacons Integration - JAL-3826
Configuration for jalview project in IntelliJ IDEA IDE - JAL-3823
Ascertain which new features in Install4j 9 will be useful - JAL-3820
In Linux desktops' task-managers, the grouped Jalview windows get a generic name - JAL-3819
Metainfo file for Jalview in Debian - JAL-3814
user preference token controlling launch of the news browser (like -nonews argument) - JAL-3811
'Discover Web Services' option to trigger a one off JABAWS discovery if autodiscovery was disabled - JAL-3805
Remove the Old Jalview Uninstaller application from the DMG - JAL-3796
Notarize Jalview OSX installers - JAL-3794
X should be recognised as the unknown base in DNA sequences - JAL-3793
Improve filter for heteroatom ligands when importing chains from structure - JAL-3788
NPE in Overview colouring as ClustalX on New View with automatic Overview - JAL-3784
Closing Overview may null the wrong AlignPanel's overview reference - JAL-3780
jalview hangs and becomes unusable when mouse hovering over sequence with structure shown in chimera and horizontal scrolling with trackpad - JAL-3779
Annotation file: PROPERTIES apply only to the first SEQUENCE_GROUP defined - JAL-3775
Merge of some 2.11.1.3 issues to develop - JAL-3771
CDS aligned in Aligned CDS/Protein view shown via 'show crossrefs->Uniprot' does not match protein alignment - JAL-3770
Sequence font resolution appears lower than other rendered fonts (e.g. Column numbering and Annotation Labels) in the Alignment window when using a HiDPI display - JAL-3765
Find in 2.11.1.2 isn't reporting all matches for a regex - JAL-3764
Hide PDB RESNUM features on Chimera / non-Jmol structures - JAL-3763
Redact change that had CDS share dataset sequence of parent gene or transcript - JAL-3762
JalviewJS doesn't honour arguments passed via Info.args when there are arguments on the URL - JAL-3761
MapList.locateInFrom() gives wrong result for overlapping from ranges - JAL-3760
Alignments containing one or more protein sequences can be classed as nucleotide - JAL-3754
Deprecated Gradle features warning when building with command line
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