Jalview 2.8.0b1

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WARNING! Downloading this JVL file might automatically switch your Jalview installation to version 2.8.0b1 (without auto-updates).

To revert back to the Jalview RELEASE channel, please visit the Using the Jalview Launch file page.

Download the Jalview Launch file (.jvl) for version 2.8.0b1?


New Features

  • Trusted certificates for JalviewLite applet and Jalview Desktop application
    Certificate was donated by Certum to the Jalview open source project).
  • Jalview SRS links replaced by UniProt and EBI-search
  • Output in Stockholm format
  • Allow import of data from gzipped files
  • Export/import group and sequence associated line graph thresholds
  • Nucleotide substitution matrix that supports RNA and ambiguity codes
  • Allow disorder predictions to be made on the current selection (or visible selection) in the same way that JPred works
  • Groovy scripting for headless Jalview operation

Other improvements

  • Upgrade desktop installer to InstallAnywhere 2013
  • COMBINE statement uses current SEQUENCE_REF and GROUP_REF scope to group annotation rows
  • Support ’’ style escaping of quotes in Newick files
  • Group options for JABAWS service by command line name
  • Empty tooltip shown for JABA service options with a link but no description
  • Select primary source when selecting authority in database fetcher GUI
  • Add .mfa to FASTA file extensions recognised by Jalview
  • Annotation label tooltip text wrap

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