Release History

- General -

Improved memory usage: sparse arrays used for all consensus calculations

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

Sequence ID tool tips have been tamed (databases sorted alphabetically, abridged ID sets)
New replacement token for creating URLs just from database cross references. Users with custom links will receive a warning dialog asking them to update their preferences.
Cancel button and escape listener on dialog warning user about disconnecting Jalview from a Chimera session
Custom URL links for database cross-references are matched to database name regardless of case
+ + 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

Build and deployment

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

Columns with more than one modal residue are not coloured or thresholded according to percent identity (first observed in Jalview 2.8.2)
Threonine incorrectly reported as not hydrophobic
Updates to documentation pages (above PID threshold, amino acid properties)
Lower case residues in sequences are not reported as mapped to residues in a structure file in the View Mapping report
+ 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

Custom URL links for specific database names without regular expressions also offer invalid links from Sequence ID
Removing a single configured link in the URL links pane in Connections preferences doesn't actually update Jalview configuration
CTRL-Click on a selected region to open the alignment area popup menu doesn't work on El-Capitan
Jalview doesn't offer to associate mmCIF files with similarly named sequences if dropped onto the alignment
Additional mappings are shown for PDB entries where more chains exist in the PDB accession than are reported in the SIFTS file
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

- Build and deployment + New Known Issues

Failing/passing unit tests
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

- New Known Issues + Test Suite +

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

+ General +

+ Columns with more than one modal residue + are not coloured or thresholded according to percent + identity (first observed in Jalview 2.8.2) +
+ Threonine incorrectly reported as not + hydrophobic +
+ Updates to documentation pages (above PID + threshold, amino acid properties) +
+ Lower case residues in sequences are not + reported as mapped to residues in a structure file in the + View Mapping report +
+ Identical features with non-numeric scores + could be added multiple times to a sequence +
+ Disulphide + bond features shown as two highlighted residues rather + than a range in linked structure views, and treated + correctly when selecting and computing trees from features +
+ Custom URL links for database + cross-references are matched to database name regardless + of case +

+ Application +

+ Custom URL links for specific database + names without regular expressions also offer links from + Sequence ID +
+ Removing a single configured link in the + URL links pane in Connections preferences doesn't actually + update Jalview configuration +
+ CTRL-Click on a selected region to open + the alignment area popup menu doesn't work on El-Capitan +
+ Jalview doesn't offer to associate mmCIF + files with similarly named sequences if dropped onto the + alignment +
+ Additional mappings are shown for PDB + entries where more chains exist in the PDB accession than + are reported in the SIFTS file +
+ Certain structures do not get mapped to + the structure view when displayed with Chimera +
+ No chains shown in the Chimera view + panel's View->Show Chains submenu +
+ Export as HTML with embedded SVG doesn't + work for wrapped alignment views +
+ Rename UI components for running JPred + predictions from 'JNet' to 'JPred' +
+ Export as PNG or SVG is + corrupted when annotation panel vertical scroll is not at + first annotation row +
+ Attempting to view structure for Hen + lysozyme results in a PDB Client error dialog box +
+ Structure View's mapping report switched ranges for PDB and sequence for SIFTS