Release History

+ General +

+ Application +

+ Sequence ID tool tip presents abridged + set of database cross-references, sorted alphabetically +
+ 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 +
+ Jalview's Chimera control window closes if + the Chimera it is connected to is shut down +
+ 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 +

+ 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 +

+ +

+ General +

Colour by conservation always enabled and no tick + shown in menu when BLOSUM or PID shading applied
FER1_ARATH and FER2_ARATH labels were switched in + example sequences/projects/trees

Application

Cannot import or associated local PDB files without a PDB ID HEADER line
RMSD is not output in Jmol console when superposition is performed
Drag and drop of URL from Browser fails for Linux and OSX versions earlier than El Capitan
Jalview projects with views of local PDB structure + files saved on Windows cannot be opened on OSX
Multiple structure views can be opened and + superposed without timeout for structures with multiple + models or multiple sequences in alignment
Cannot import or associated local PDB files without + a PDB ID HEADER line
RMSD is not output in Jmol console when + superposition is performed
Drag and drop of URL from Browser fails for Linux + and OSX versions earlier than El Capitan
ENA client ignores invalid content from ENA server
Exceptions are not raised when ENA client attempts to fetch non-existent IDs via Fetch DB Refs UI option
Exceptions are not raised when a new view is created on the alignment
Exceptions are not raised in console when ENA + client attempts to fetch non-existent IDs via Fetch DB + Refs UI option
Exceptions are not raised in console when a new + view is created on the alignment
OSX right-click fixed for group selections: + CMD-click to insert/remove gaps in groups and CTRL-click + to open group pop-up menu

- New Known Issues -

Build and deployment -

+ New Known Issues +