Version 2.10.0


Thank you to everyone who wrote letters of support last year for our application to the BBSRC, we should hear the outcome in the next couple of months.

We are now applying to the Wellcome Trust to renew funding to support Jalview's use in biomedical sequence analysis, including interpretation of genomic variation and long read RNA data (e.g. Nanopore) at the protein coding level. If you would like Jalview to continue to develop and be supported 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 22nd March 2019.

Thank you!

Version Date: 
06-10-2016

New Features

General

  • Updated Spanish translations.
  • Jmol now primary parser for importing structure data to Jalview. Enables mmCIF and better PDB parsing.
  • Alignment ruler shows positions relative to reference sequence
  • Position/residue shown in status bar when mousing over sequence associated annotation
  • Default RNA SS symbol to 'matching bracket' for manual entry
  • RNA Structure consensus indicates wc-only '()', canonical '[]' and invalid '{}' base pair populations for each column
  • Feature settings popup menu options for showing or hiding columns containing a feature
  • Edit selected group by double clicking on group and sequence associated annotation labels
  • Sequence name added to annotation label in select/hide columns by annotation and colour by annotation dialogs

Application

  • Automatically hide introns when opening a gene/transcript view
  • Uniprot Sequence fetcher Free Text Search dialog
  • UniProt - PDB protein structure mappings with the EMBL-EBI PDBe SIFTS database
  • Updated download sites used for Rfam and Pfam sources to xfam.org
  • Disabled Rfam(Full) in the sequence fetcher
  • Show residue labels in Chimera when mousing over sequences in Jalview
  • Support for reverse-complement coding regions in ENA and EMBL
  • Upgrade to EMBL XML 1.2 for record retrieval via ENA rest API
  • Support for ENA CDS records with reverse complement operator
  • Update to groovy-2.4.6-indy - for faster groovy script execution
  • New 'execute Groovy script' option in an alignment window's Calculate menu
  • Allow groovy scripts that call Jalview.getAlignFrames() to run in headless mode
  • Support for creating new alignment calculation workers from groovy scripts
  • Store/restore reference sequence in Jalview projects
  • Chain codes for a sequence's PDB associations are now saved/restored from project
  • Database selection dialog always shown before sequence fetcher is opened
  • Double click on an entry in Jalview's database chooser opens a sequence fetcher
  • Free-text search client for UniProt using the UniProt REST API
  • -nonews command line parameter to prevent the news reader opening
  • Displayed columns for PDBe and Uniprot querying stored in preferences
  • Pagination for displaying PDBe and Uniprot search results
  • Tooltips shown on database chooser
  • Reverse complement function in calculate menu for nucleotide sequences
  • Alignment sort by feature scores and feature counts preserves alignment ordering (and debugged for complex feature sets).
  • Chimera 1.11.1 minimum requirement for viewing structures with Jalview 2.10
  • Retrieve genome, transcript CCDS and gene ids via the Ensembl and Ensembl Genomes REST API
  • Protein sequence variant annotation computed for 'sequence_variant' annotation on CDS regions (Ensembl)
  • ENA CDS 'show cross references' for Uniprot sequences
  • Improved warning messages when DB Ref Fetcher fails to match, or otherwise updates sequence data from external database records.
  • Revised Jalview Project format for efficient recovery of sequence coding and alignment annotation relationships.

 

Issues Resolved

General

  • reinstate CTRL-click for opening pop-up menu on OSX
  • Export features in Jalview format (again) includes graduated colourschemes
  • More responsive when working with big alignments and lots of hidden columns
  • Hidden column markers not always rendered at right of alignment window
  • Tidied up links in help file table of contents
  • Feature based tree calculation not shown for DNA alignments
  • Hidden columns ignored during feature based tree calculation
  • Alignment view stops updating when show unconserved enabled for group on alignment
  • Cannot insert gaps into sequence when set as reference
  • Alignment column in status incorrectly shown as "Sequence position" when mousing over annotation
  • Incorrect column numbers in ruler when hidden columns present
  • Colour by RNA Helices not enabled when user created annotation added to alignment
  • RNA Structure consensus only computed for '()' base pair annotation
  • Enabling 'Ignore Gaps' results in zero scores for all base pairs in RNA Structure Consensus
  • Extend selection with columns containing feature not working
  • Pfam format writer puts extra space at beginning of sequence
  • Incomplete sequence extracted from pdb entry 3a6s
  • Cannot create groups on an alignment from from a tree when t-coffee scores are shown
  • Cannot import and view PDB structures with chains containing negative resnums (4q4h)
  • ArithmeticExceptions raised when parsing some structures
  • 'Empty' alignment blocks added to Clustal, PIR and PileUp output
  • Reordering sequence features that are not visible causes alignment window to repaint
  • Threshold sliders don't work in graduated colour and colour by annotation row for e-value scores associated with features and annotation rows
  • amino acid physicochemical conservation calculation should be case independent
  • Remove annotation also updates hidden columns
  • FER1_ARATH and FER2_ARATH mislabelled in example file (uniref50.fa, feredoxin.fa, unaligned.fa, exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
  • Null pointer exceptions and redraw problems when reference sequence defined and 'show non-conserved' enabled
  • Quality and Conservation are now shown on load even when Consensus calculation is disabled

Application

  • URLs and links can't be imported by drag'n'drop on OSX when launched via webstart (note - not yet fixed for El Capitan)
  • Corrupt preferences for SVG, EPS & HTML output when running on non-gb/us i18n platforms
  • Error thrown when exporting a view with hidden sequences as flat-file alignment
  • InstallAnywhere distribution fails when launching Chimera
  • Jalview very slow to launch via webstart (also hotfix for 2.9.0b2)
  • Cannot save project when view has a reference sequence defined
  • Columns are suddenly selected in other alignments and views when revealing hidden columns
  • Hide columns not mirrored in complement view in a cDNA/Protein splitframe
  • Cannot save/restore representative sequence from project when only one sequence is represented
  • Disabled 'Best Uniprot Coverage' option in Structure Chooser
  • Modifying 'Ignore Gaps' on consensus or structure consensus didn't refresh annotation panel
  • View mapping in structure view shows mappings between sequence and all chains in a PDB file
  • PDB and Uniprot FTS dialogs format columns correctly, don't display array data, sort columns according to type
  • Export complete shown after destination file chooser is cancelled during an image export
  • Error when querying PDB Service with sequence name containing special characters
  • Manual PDB structure querying should be case insensitive
  • Large tooltips with broken HTML formatting don't wrap
  • Figures exported from wrapped view are truncated so L looks like I in consensus annotation
  • Export features should only export the currently displayed features for the current selection or view
  • Enable 'Get Cross-References' in menu after fetching cross-references, and restoring from project
  • Mouseover of a copy of a sequence is not followed in the structure viewer
  • Titles for individual alignments in splitframe not restored from project
  • missing autocalculated annotation at trailing end of protein alignment in transcript/product splitview when pad-gaps not enabled by default
  • amino acid physicochemical conservation is case dependent
  • RSS reader doesn't stay hidden after last article has been read (reopened issue due to internationalisation problems)
  • Only offer PDB structures in structure viewer based on sequence name, PDB and UniProt cross-references
  • No progress bar shown during export of alignment as HTML
  • Structures not always superimposed after multiple structures are shown for one or more sequences.
  • Reference sequence characters should not be replaced with '.' when 'Show unconserved' format option is enabled.
  • Cannot specify chain code when entering specific PDB id for sequence
  • File->Export->.. as doesn't work when 'Export hidden sequences' is enabled, but 'export hidden columns' is disabled.
  • Best Quality option in structure chooser selects lowest rather than highest resolution structures for each sequence
  • Incorrect start and end reported for PDB to sequence mapping in 'View Mappings' report

    • RNA 3D structure not added via DSSR service

Applet

  • Incorrect columns are selected when hidden columns present before start of sequence
  • Missing dependencies on applet pages (JSON jars)
  • Overview pixel size changes when sequences are hidden in applet
  • Updated instructions for applet deployment on examples pages.
  • Duplicate group consensus and conservation rows shown when tree is partitioned
  • Erratic behaviour when tree partitions made with multiple cDNA/Protein split views