Version 2.10.0

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