--- channel: release version: 2.10.0 date: 2016-10-06 --- ## 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 - Remove right on penultimate column of alignment does nothing ### 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 - Unable to read old Jalview projects that contain non-XML data added after Jalvew wrote project. - Newly created annotation row reorders after clicking on it to create new annotation for a column. - Null Pointer Exception raised when pressing Add on an orphaned cut'n'paste window. ### 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.