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