Release History

+ General +

Revised implementation of PCA for speed and memory efficiency (~30x faster)
Trees computed on Sequence Feature Similarity may have different topology due to increased precision
More robust colours and shader model for alignments and groups
Custom shading schemes created via groovy scripts
linked scrolling of CDS/Protein views via Overview or sequence motif search operations
Efficiency improvements for interacting with alignment and overview windows
Hidden columns and sequences can be omitted in Overview
+ Posterior probability annotation from + Stockholm files imported as sequence associated annotation +
+ Sequence names don't include file + extension when importing structure files without embedded + names or PDB accessions +
Amend sequence features dialog box can be opened by double clicking gaps within sequence feature extent
Graduated feature colour style example included in the example feature file

+ Application +

+ + Experimental Features Checkbox in Desktop's Tools + menu to hide or show untested features in the application. +
Warning in alignment status bar when there are not enough columns to superimpose structures in Chimera
Faster Chimera/Jalview communication by file-based command exchange
URLs for viewing database cross-references provided by identifiers.org and the EMBL-EBI's MIRIAM DB
Updated JABAWS client to v2.2

+ Experimental features +

+ New entries in the Chimera menu + to transfer Chimera's structure attributes as Jalview + features, and vice-versa. +

+ Applet +

+ Test Suite +

Added PrivilegedAccessor to test suite
Prevent or clear modal dialogs raised during tests
+ Scripting +
- FileFormatI interface for describing and identifying file formats (instead of String constants)
+

+ General +

+ Fixed incorrect value in BLOSUM 62 score + matrix - C->R should be '-3'
Old matrix restored with + this one-line groovy script:
jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3 +
+ Fixed Jalview's treatment of gaps in PCA + and substitution matrix based Tree calculations.
In + earlier versions of Jalview, gaps matching gaps were + penalised, and gaps matching non-gaps penalised even more. + In the PCA calculation, gaps were actually treated as + non-gaps - so different costs were applied, which meant + Jalview's PCAs were different to those produced by + SeqSpace.
Jalview now treats gaps in the same way as + SeqSpace (ie it scores them as 0). To restore pre-2.10.2 + behaviour
+ jalview.viewmodel.PCAModel.scoreGapAsAny=true // for + 2.10.1 mode
+ jalview.viewmodel.PCAModel.scoreGapAsAny=false // to + restore 2.10.2 mode +
Reopening Colour by annotation dialog doesn't reselect a specific sequence's associated annotation after it was used for colouring a view
Hidden regions in alignment views are not coloured in linked structure views
Current selection lost if popup menu opened on a region of alignment without groups
Popup menu not always shown for regions of an alignment with overlapping groups
Finder double counts if both a sequence's name and description match
Hiding column selection containing two hidden regions results in incorrect hidden regions
PCA calculation could hang when generating output report when working with highly redundant alignments
Cannot configure feature colours with lightGray or darkGray via features file
Overview window visible region moves erratically when hidden rows or columns are present
Per-residue colourschemes applied via the Structure Viewer's colour menu don't correspond to sequence colouring
Protein specific colours only offered in colour and group colour menu for protein alignments
'Apply to all groups' setting when changing colour does not apply Conservation slider value to all groups
Colour threshold slider doesn't update to reflect currently selected view or group's shading thresholds
Percentage identity and conservation menu items do not show a tick or allow shading to be disabled
Conservation shading or PID threshold lost when base colourscheme changed if slider not visible
Sequence features shown in tooltip for gaps before start of features
Very large alignments take a long time to load
Graduated feature colour threshold not restored to UI when feature colour is edited
Feature colour thresholds not respected when rendered on overview and structures when opacity at 100%
Structure and alignment overview update as graduate feature colour settings are modified via the dialog box
Vertical scrollbar jumps one page-width at a time when scrolling vertically in wrapped mode.
Overview window doesn't always update when a group defined on the alignment is resized
Mouseovers on left/right scale region in wrapped view result in positional status updates
Status bar shows position for ambiguous amino acid and nucleotide symbols
Copy consensus sequence failed if alignment included gapped columns
User defined gap colour not shown in overview when features overlaid on alignment

+ Documentation +

Release notes reformatted for readibility with the built-in Java help viewer

+ Application +

Easier creation of colours for all 'Lower case' residues (button in colourscheme editor debugged and new documentation and tooltips added)
Text colour threshold's 'Cancel' button doesn't restore group-specific text colour thresholds
Feature settings panel does not update as new features are added to alignment
Structure viewer's View -> Colour By view selection menu changes colours of alignment views
Proxy server address and port always appear enabled in Preferences->Connections
Spurious exceptions in console raised from alignment calculation workers after alignment has been closed
Typo in selection popup menu - Create groups now 'Create Group'
CMD/CTRL and G or Shift G for Create/Undefine group doesn't always work
Tree Viewer's Print Dialog doesn't get shown again after pressing 'Cancel'
DAS registry not found exceptions removed from console output
Above PID colour threshold not recovered when alignment view imported from project
No mappings generated between structure and sequences extracted from structure files imported via URL
+ Structures loaded via URL are saved in + Jalview Projects rather than fetched via URL again when + the project is loaded and the structure viewed +
Trackpad horizontal scroll gesture adjusts start position in wrap mode
Status bar doesn't show positions for ambiguous amino acids
Hide insertions in PopUp menu excludes gaps in selection, current sequence and only within selected columns
Cannot retrieve protein products from Ensembl by Peptide ID
cDNA Consensus annotation not shown in CDS/Protein view after CDS sequences added for aligned proteins

+ Applet +

Switching between Nucleotide and Protein score models doesn't always result in an updated PCA plot
Features not rendered as transparent on overview or linked structure view
Colour group by conservation doesn't work (since 2.8)
Hitting Cancel after applying user-defined colourscheme doesn't restore original colourscheme

+ New Known Issues +

Protein/CDS view scrolling not always in phase after a sequence motif find operation
Importing annotation file with rows containing just upper and lower case letters are interpreted as WUSS rna secondary structure symbols
Cannot load Newick trees from eggnog ortholog database

+ Test Suite +

Unit test failure: jalview.ws.jabaws.RNAStructExportImport setup fails