Issues Resolved

• Slow scrolling when lots of annotation rows are displayed
• Lots of NPE (and slowness) after creating RNA secondary structure annotation line
• Sequence database accessions not imported when fetching alignments from Rfam
• Incorrect SHMR submission for sequences with identical IDs
• View all structures does not always superpose structures
• Option widgets in service parameters not updated to reflect user or preset settings
• Null pointer exceptions for some services without presets or adjustable parameters
• Discover PDB IDs entry in structure menu doesn’t discover PDB xRefs
• Exception encountered while trying to retrieve features with DAS
• Lowest value in annotation row isn’t coloured when colour by annotation (per sequence) is coloured
• Keyboard mode P jumps to start of gapped region when residue follows a gap
• Jalview appears to hang importing an alignment with Wrap as default or after enabling Wrap
• ‘Right click to add annotations’ message shown in wrap mode when no annotations present
• Disorder predictions fail with NPE if no automatic annotation already exists on alignment
• oninit javascript function should be called after initialisation completes
• Remove redundancy after disorder prediction corrupts alignment window display
• Example annotation file in documentation is invalid
• Grouped line graph annotation rows are not exported to annotation file
• Multi-harmony analysis cannot be run when only two groups created
• Cannot create multiple groups of line graphs with several ‘combine’ statements in annotation file
• Pressing return several times causes Number Format exceptions in keyboard mode
• Multi-harmony (SHMMR) method doesn’t submit correct partitions for input data
• Translation from DNA to Amino Acids fails
• Jalview fail to load newick tree with quoted label
• –headless flag isn’t understood
• ClassCastException when generating EPS in headless mode
• Adjusting sequence-associated shading threshold only changes one row’s threshold
• Preferences and Feature settings panel panel doesn’t open
• hide consensus histogram also hides conservation and quality histograms