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