Issues Resolved

Application

• logo keeps spinning and status remains at queued or running after job is cancelled
• cannot export features from alignments imported from Jalview/VAMSAS projects
• Buggy slider for web service parameters that take float values
• Newly created RNA secondary structure line doesn’t have ‘display all symbols’ flag set
• T-COFFEE alignment score shading scheme and other annotation shading not saved in Jalview project
• Local file cannot be loaded in freshly downloaded Jalview
• Jalview icon not shown on dock in Mountain Lion/Webstart
• Load file from desktop file browser fails
• Occasional NPE thrown when calculating large trees
• Cannot reorder or slide sequences after dragging an alignment onto desktop
• Colour by annotation dialog throws NPE after using ’extract scores’ function
• Loading/cut’n’pasting an empty file leads to a grey alignment window
• Disorder thresholds rendered incorrectly after performing IUPred disorder prediction
• Multiple group annotated consensus rows shown when changing ’normalise logo’ display setting
• Find shows blank dialog after ‘finished searching’ if nothing matches query
• Null Pointer Exceptions raised when sorting by feature with lots of groups
• Errors in Jmol console when structures in alignment don’t overlap
• Not all working JABAWS services are shown in Jalview’s menu
• JAVAWS version of Jalview fails to launch with ‘invalid literal/length code’
• Annotation/RNA Helix colourschemes cannot be applied to alignment with groups (actually fixed in 2.8.0b1)
• RNA Helices and T-Coffee Scores available as default colourscheme

Applet

• Remove group option is shown even when selection is not a group
• Apply to all groups ticked but colourscheme changes don’t affect groups
• Documented RNA Helices and T-Coffee Scores as valid colourscheme name
• Annotation labels drawn on sequence IDs when Annotation panel is not displayed
• Increased font size for dropdown menus on OSX and embedded windows

Other

• Consensus sequence for alignments/groups with a single sequence were not calculated
• annotation files that contain only groups imported as annotation and junk sequences
• Fasta files with sequences containing ‘*’ incorrectly recognised as PFAM or BLC
• conservation/PID slider apply all groups option doesn’t affect background (2.8.0b1)
• redundancy highlighting is erratic at 0% and 100%
• Remove gapped columns fails for sequences with ragged trailing gaps
• AMSA annotation row with leading spaces is not registered correctly on import
• Jalview crashes when selecting PCA analysis for certain alignments
• Opening the colour by annotation dialog for an existing annotation based ‘use original colours’ colourscheme loses original colours setting