--- /dev/null
+---
+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<br/>
+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
git://source.jalview.org / jalview.git / blobdiff