Issues Resolved

• Alignment prettyprinter doesn’t cope with long sequence IDs
• clustalx colourscheme colours Ds preferentially when both D+E are present in over 50% of the column
• nucleic acid structures retrieved from PDB do not import correctly
• More columns get selected than were clicked on when a number of columns are hidden
• annotation label popup menu not providing correct add/hide/show options when rows are hidden or none are present
• Stockholm format shown in list of readable formats, and parser copes better with alignments from RFAM.
• CSV output of consensus only includes the percentage of all symbols if sequence logo display is enabled

Applet

• annotation panel disappears when annotation is hidden/removed

Application

• Alignment view not redrawn properly when new alignment opened where annotation panel is visible but no annotations are present on alignment
• pasted region containing hidden columns is incorrectly displayed in new alignment window
• Jalview slow to complete operations when stdout is flooded (fix is to close the Jalview console)
• typo in AlignmentFrame->View->Hide->all but selected Rregions menu item.
• inconsistent group submenu and Format submenu entry ‘Un’ or ‘Non’conserved
• Sequence feature settings are being shared by multiple distinct alignments
• group annotation not recreated when tree partition is changed
• double click on group annotation to select sequences does not propagate to associated trees
• Mac OSX specific issues:
  • exception raised when mouse clicked on desktop window background
  • Desktop menu placed on menu bar and application name set correctly
  • sequence feature settings not wide enough for the save feature colourscheme button