Version 2.10.0

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