Jalview 2.10.5 is a minor release that includes critical patches for users working with Ensembl, RNA secondary structure annotation, and those running Jalview on OSX with Java 10.
- Default memory for Jalview webstart and InstallAnywhere increased to 1G.
- Hidden sequence markers and representative sequence bolding included when exporting alignment as EPS, SVG, PNG or HTML. Display is configured via the Format menu, or for command-line use via a jalview properties file.
- Ensembl client updated to Version 7 REST API and sequence data now imported as JSON.
- Change in recommended way of starting Jalview via a Java command line: add jars in lib directory to CLASSPATH, rather than via the deprecated java.ext.dirs property.
- Support added to execute test suite instrumented with Open Clover
- Poorly scaled bar in quality annotation row shown in Feredoxin Structure alignment view of example alignment.
- Annotation obscures sequences if lots of annotation displayed.
- Group conservation/consensus not shown for newly created group when 'Apply to all groups' selected.
- Corrupted display when switching to wrapped mode when sequence panel's vertical scrollbar is visible.
- Alignment is black in exported EPS file when sequences are selected in exported view.
- Groups with different coloured borders aren't rendered with correct colour.
- Jalview could hang when importing certain types of knotted RNA secondary structure.
- Sequence highlight and selection in trimmed VARNA 2D structure is incorrect for sequences that do not start at 1.
- '.' inserted into RNA secondary structure annotation when columns are inserted into an alignment, and when exporting as Stockholm flatfile.
- Jalview annotation rows containing upper and lower-case 'E' and 'H' do not automatically get treated as RNA secondary structure.
- .jvp should be used as default extension (not .jar) when saving a jalview project file.
- Mac Users: closing a window correctly transfers focus to previous window on OSX
Java 10 Issues Resolved
- OSX - Can't save new files via the File or export menus by typing in a name into the Save dialog box.
- Jalview now uses patched version of the VAqua5 'look and feel' which has improved compatibility with the latest version of OSX.