--- channel: release version: 2.9 date: 2015-09-10 --- ## New Features ### General - Linked visualisation and analysis of DNA and Protein alignments: - Translated cDNA alignments shown as split protein and DNA alignment views - Codon consensus annotation for linked protein and cDNA alignment views - Link cDNA or Protein product sequences by loading them onto Protein or cDNA alignments - Reconstruct linked cDNA alignment from aligned protein sequences - Jmol integration updated to Jmol v14.2.14 - Import and export of Jalview alignment views as [BioJSON](features/bioJsonFormat.html) - New alignment annotation file statements for reference sequences and marking hidden columns - Reference sequence based alignment shading to highlight variation - Select or hide columns according to alignment annotation - Find option for locating sequences by description - Conserved physicochemical properties shown in amino acid conservation row - Alignments can be sorted by number of RNA helices ### Application - New cDNA/Protein analysis capabilities - Get Cross-References should open a Split Frame view with cDNA/Protein - Detect when nucleotide sequences and protein sequences are placed in the same alignment - Split cDNA/Protein views are saved in Jalview projects - Use REST API to talk to Chimera - Selected regions in Chimera are highlighted in linked Jalview windows - VARNA RNA viewer updated to v3.93 - VARNA views are saved in Jalview Projects - Pseudoknots displayed as Jalview RNA annotation can be shown in VARNA - Make groups for selection uses marked columns as well as the active selected region - Calculate UPGMA and NJ trees using sequence feature similarity - New Export options - New Export Settings dialog to control hidden region export in flat file generation - Export alignment views for display with the [BioJS MSAViewer](http://msa.biojs.net/) - Export scrollable SVG in HTML page - Optional embedding of BioJSON data when exporting alignment figures to HTML - 3D structure retrieval and display - Free text and structured queries with the PDBe Search API - PDBe Search API based discovery and selection of PDB structures for a sequence set - JPred4 employed for protein secondary structure predictions - Hide Insertions menu option to hide unaligned columns for one or a group of sequences - Automatically hide insertions in alignments imported from the JPred4 web server - (Nearly) Native 'Quaqua' dialogs for browsing file system on OSX
LGPL libraries courtesy of [http://www.randelshofer.ch/quaqua/](http://www.randelshofer.ch/quaqua/) - changed 'View nucleotide structure' submenu to 'View VARNA 2D Structure' - change "View protein structure" menu option to "3D Structure ..." ### Applet - New layout for applet example pages - New parameters to enable SplitFrame view (file2,enableSplitFrame, scaleProteinAsCdna) - New example demonstrating linked viewing of cDNA and Protein alignments ### Development and deployment - Java 1.7 minimum requirement for Jalview 2.9 - Include installation type and git revision in build properties and console log output - Jalview Github organisation, and new github site for storing BioJsMSA Templates - Jalview's unit tests now managed with TestNG ## Issues Resolved ### Application - Escape should close any open find dialogs - Typo in select-by-features status report - Consensus RNA secondary secondary structure predictions are not highlighted in amber - Missing gap character in v2.7 example file means alignment appears unaligned when pad-gaps is not enabled - First switch to RNA Helices colouring doesn't colour associated structure views - ID width preference option is greyed out when auto width checkbox not enabled - Stopped a warning dialog from being shown when creating user defined colours - 'View Mapping' in structure viewer shows sequence mappings for just that viewer's sequences - Workaround for superposing PDB files containing multiple models in Chimera - Report sequence position in status bar when hovering over Jmol structure - Cannot output gaps as '.' symbols with Selection -> output to text box - Flat file exports of alignments with hidden columns have incorrect sequence start/end - 'Aligning' a second chain to a Chimera structure from Jalview fails - Colour schemes applied to structure viewers don't work for nucleotide - Loading/cut'n'pasting an empty or invalid file leads to a grey/invisible alignment window - Exported Jpred annotation from a sequence region imports to different position - Space at beginning of sequence feature tooltips shown on some platforms - Chimera viewer 'View | Show Chain' menu is not populated - 'New View' fails with a Null Pointer Exception in console if Chimera has been opened - Mouseover to Chimera not working - Miscellaneous ENA XML feature qualifiers not retrieved - NPE in annotation renderer after 'Extract Scores' - If two structures in one Chimera window, mouseover of either sequence shows on first structure - 'Show annotations' options should not make non-positional annotations visible - Subsequence secondary structure annotation not shown in right place after 'view flanking regions' - File Save As type unset when current file format is unknown - Save as '.jar' option removed for saving Jalview projects - Colour by Sequence colouring in Chimera more responsive - Cannot 'add reference annotation' for a sequence in several views on same alignment - Cannot show linked products for EMBL / ENA records - Jalview's tooltip wraps long texts containing no spaces ### Applet - Jmol to JalviewLite mouseover/link not working - JalviewLite can't import sequences with ID descriptions containing angle brackets ### General - Cannot export and reimport RNA secondary structure via jalview annotation file - Random helix colour palette for colour by annotation with RNA secondary structure - Mouseover to cDNA from STOP residue in protein translation doesn't work. - hints when using the select by annotation dialog box - Jmol alignment incorrect if PDB file has alternate CA positions - FontChooser message dialog appears to hang after choosing 1pt font - Peptide secondary structure incorrectly imported from annotation file when annotation display text includes 'e' or 'h' - Cannot set colour of new feature type whilst creating new feature - cDNA translation alignment should not be sequence order dependent - 'Show unconserved' doesn't work for lower case sequences - Nucleotide ambiguity codes involving R not recognised ### Deployment and Documentation - Applet example pages appear different to the rest of www.jalview.org ### Application Known issues - Incomplete sequence extracted from PDB entry 3a6s - Misleading message appears after trying to delete solid column. - Jalview icon not shown in dock after InstallAnywhere version launches - Fetching EMBL reference for an RNA sequence results fails with a sequence mismatch - Corrupted or unreadable alignment display when scrolling alignment to right - ArrayIndexOutOfBoundsException thrown when remove empty columns called on alignment with ragged gapped ends - auto calculated alignment annotation rows do not get placed above or below non-autocalculated rows - Jalview dekstop becomes sluggish at full screen in ultra-high resolution - Cannot disable consensus calculation independently of quality and conservation - Mouseover highlighting between cDNA and protein can become sluggish with more than one splitframe shown ### Applet Known Issues - Core PDB parsing code requires Jmol - Sequence canvas panel goes white when alignment window is being resized