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- JAL-4411
Record source metadata in derived/transferred annotation rows - JAL-4401
Improve alignment annotation data model - JAL-4338
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 - JAL-4313
AlignmentAnnotation#makeVisibleAnnotation produces incorrect results. - JAL-4306
SeqCigar.getSeq should return an empty sequence for 0-length sequence. - JAL-4245
Return null from getRootDatasetSequence if there is no dataset sequence - JAL-4233
nf-core/proteinfold integration - JAL-4221
sequence descriptions are updated from database reference sources if not already defined - JAL-4188
copy and paste of PAE matrix from one alignment to another doesnt work - JAL-4182
reference annotation not correctly transferred to alignment containing a sub-sequence when a selection is active - JAL-4157
Annotation colouring dialog box doesn't remember 'use original colours' settings when opened via the Colour menu - JAL-4156
Sequence associated annotation colouring should update when other sequences get annotated - JAL-4147
sub-labels for annotation rows - JAL-4129
Migrate semantics for DBRefEntry version string to support versioned sources and cross-references - JAL-3980
sequence ID tooltip not showing during long running retrieval/crossref operations - JAL-3979
improve efficiency of PDBEntry operations - JAL-3903
Improvements for comparative analysis of repeats in biomolecules - JAL-3899
Use dedicated sequence data object when uniquifying the seuqences - JAL-3880
show additional metadata along side annotation row labels - JAL-3863
Identify canonical Uniprot accessions in protein sequence cross-references - JAL-3860
propagate mouseover, region highlights and selection events on reference to transcripts and products - JAL-3856
Support extended PDB ids - JAL-3760
Alignments containing one or more protein sequences can be classed as nucleotide - JAL-3735
Space/time efficient representation of aligned sequences as CIGAR - JAL-3576
IntervalStore should preserve order of addition of co-located features - JAL-3471
Representing and Manipulating indels in Jalview - JAL-3452
SequenceFeature.isNonPositional not a valid check - JAL-3397
Alternative to NCList for IntervalStore; improvements for FeatureStore - JAL-3396
SequenceFeature begin/end sometimes handled as int, sometimes long - JAL-3365
Secondary structure annotation beyond DSSP-3 state interpreted as RNA extended base pair contacts in Stockholm files - JAL-3331
Don't repeatedly query Ensembl for products of non-coding transcripts - JAL-3324
Filter features by score or attribute value percentiles - JAL-3313
codon consensus text not scaled to fit within consensus histogram - JAL-3311
Sunset VAMSAS and rescue functionality - JAL-3251
Add biotype info to sequence mappings - JAL-3156
Alignment consensus and conservation shading should honour hidden-representative sequences - JAL-3109
Extra annotation rows appear when removing and recreating group in example project - JAL-3104
wrong value and unscaled bar in last position of quality score annotation - JAL-3016
Cannot reconstruct CDS alignment for alignment of several subsequences of a single dataset sequence - JAL-3012
Avoid duplicating data when anonymising it for export to external analysis tool - JAL-2996
treat '~' tilde as special gap character - JAL-2986
Sequence.findIndex wrong when 'end' > sequence length - JAL-2940
Deleting sequence from alignment doesn't delete it from sequence group - JAL-2880
no binding between derived annotation rows and original structure data file parsed via Jmol - JAL-2879
Save a map-valued feature attribute in Jalview project - JAL-2772
ArrayIndexOutOfBoundsException in findFeatures - JAL-2770
CigarArray documentation and testing - JAL-2765
Short isoforms from Ensembl are expanded to full length Uniprot sequences - JAL-2759
Add cursor to HiddenColumns - JAL-2742
Out by one error in CigarArray constructor
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