Version 2.10.2


Jalview is free to end-users because of support from the UK's BBSRC and The Wellcome Trust

If you would like to see Jalview continue to be available then please take a few minutes to write us a support letter saying how you use Jalview in your research/teaching.

Write as a PDF including your institution's heading and send to:
support_jalview@bartongroup.org by Friday 19th October 2018.

Thank you all those who have already written such nice letters!

Version Date: 
17-08-2017

New Features

Calculations

  • Occupancy annotation row shows number of ungapped positions in each column of the alignment.
  • Tree/PCA calculation menu items merged to a calculation dialog box
  • Revised implementation of PCA for speed and memory efficiency (~30x faster)
  • Revised implementation of sequence similarity scores as used by Tree, PCA, Shading Consensus and other calculations
  • Score matrices are stored as resource files within the Jalview codebase
  • Trees computed on Sequence Feature Similarity may have different topology due to increased precision

Rendering

  • More robust colours and shader model for alignments and groups
  • Custom shading schemes created via groovy scripts

Overview

  • Efficiency improvements for interacting with alignment and overview windows
  • Scrolling of wrapped alignment views via overview
  • Hidden columns and sequences can be omitted in Overview
  • Click-drag in visible area allows fine adjustment of visible position

Data import/export

  • Posterior probability annotation from Stockholm files imported as sequence associated annotation
  • More robust per-sequence positional annotation input/output via stockholm flatfile
  • Sequence names don't include file extension when importing structure files without embedded names or PDB accessions
  • Drag and drop load of AAIndex and NCBI format sequence substitution matrices

User Interface

  • Experimental Features Checkbox in Desktop's Tools menu to hide or show untested features in the application.
  • Linked scrolling of CDS/Protein views via Overview or sequence motif search operations
  • Amend sequence features dialog box can be opened by double clicking gaps within sequence feature extent
  • Status bar message shown when not enough aligned positions were available to create a 3D structure superposition.

3D Structure

  • Hidden regions in alignment views are not coloured in linked structure views
  • Faster Chimera/Jalview communication by file-based command exchange
  • Structure chooser automatically shows Cached Structures rather than querying the PDBe if structures are already available for sequences
  • Structures imported via URL are cached in the Jalview project rather than downloaded again when the project is reopened.
  • New entries in the Chimera menu to transfer Chimera's structure attributes as Jalview features, and vice-versa (Experimental Feature)

Web Services

  • Updated JABAWS client to v2.2
  • Filter non-standard amino acids and nucleotides when submitting to AACon and other MSA Analysis services
  • URLs for viewing database cross-references provided by identifiers.org and the EMBL-EBI's MIRIAM DB

Scripting

  • FileFormatI interface for describing and identifying file formats (instead of String constants)
  • FeatureCounter script refactored for efficiency when counting all displayed features (not backwards compatible with 2.10.1)

Example files

  • Graduated feature colour style example included in the example feature file

Documentation

  • Release notes reformatted for readability with the built-in Java help viewer
  • Find documentation updated with 'search sequence description' option

Test Suite

  • External service integration tests for Uniprot REST Free Text Search Client
  • Added PrivilegedAccessor to test suite
  • Prevent or clear modal dialogs raised during tests

Issues Resolved

Calculations

User Interface

Rendering

Data import/export

Web Services

Application UI

Applet

Test Suite

New Known Issues