Release History

+ General +

More robust colours and shader model for alignments and groups
Custom shading schemes created via groovy scripts

+ 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

+ Experimental features +

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

+ Applet +

+ Test Suite +

Added PrivelegedAccessor to test suite

Prevent or clear modal dialogs raised during tests

+ +

+ General +

+ Fixed incorrect value in BLOSUM 62 score + matrix - C->R should be '3'
Old matrix restored with + this one-line groovy script:
jalview.schemes.ResidueProperties.BLOSUM62[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 mean't + 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

+ 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

+ Applet +

Features not rendered as transparent on overview or linked structure view
Colour group by conservation doesn't work (since 2.8)

+ New Known Issues +

+ +

@@ -59,19 +190,16 @@ for all consensus calculations

- Updated Jmol shipped with applet and - desktop to 14.6.4 -

- + Jmol updated to version 14.6.4 (released 3rd Oct 2016)

- +

Updated Jalview's Certum code signing certificate + for 2016-2017

Application

- Sequence ID tool tips have been tamed - (databases sorted alphabetically, abridged ID sets) + Sequence ID tool tip presents abridged + set of database cross-references, sorted alphabetically
New replacement token for creating URLs just @@ -85,35 +213,20 @@ Chimera session
- Jalview's chimera control window closes if + Jalview's Chimera control window closes if the Chimera it is connected to is shut down
- Custom URL links for database - cross-references are matched to database name regardless - of case -
- Select highlighted columns menu item and - keystroke (B) to mark columns containing highlighted - regions from structure selections or results of a Find - operation + New keystroke (B) and Select highlighted + columns menu item to mark columns containing + highlighted regions (e.g. from structure selections or results + of a Find operation)
Command line option for batch-generation of HTML pages rendering alignment data with the BioJS MSAviewer

- Applet -

- - Build and deployment -

Updated Jalview's Certum code signing certificate - for 2016-2017