- <li>Fetch DB References capabilities and UI expanded to support retrieval from DAS sequence sources</li>
- <li>Local DAS Sequence sources can be added via the command line or via the Add local source dialog box.</li>
- <li>Enable or disable non-positional feature and database references in sequence ID tooltip from View menu in application.
- </li>
- <li>URL links generated from description line for regular-expression based URL links (applet and application)
- </li>
- <li>Non-positional features displayed in sequence ID tooltip on applet
- </li>
- <li>Non-positional feature URL links are shown in link menu (applet and application)
- </li>
- <li>Automatic Scrolling option in View menu to display the currently highlighted region of an alignment.
- </li>
- <li>Improved VAMSAS synchronization (jalview archive used to preserve views, structures, and tree display settings)
- </li>
- <li>Sharing of selected regions between views and with other VAMSAS applications (Experimental feature!)
- </li>
- <li>New hidden columns and rows and representatives capabilities in annotations file (in progress - not yet fully implemented)</li>
- <li>Order an alignment in order of average feature score or total feature count</li>
+ <li>Fetch DB References capabilities and UI expanded to support
+ retrieval from DAS sequence sources</li>
+ <li>Local DAS Sequence sources can be added via the command line
+ or via the Add local source dialog box.</li>
+ <li>Enable or disable non-positional feature and database
+ references in sequence ID tooltip from View menu in application.</li>
+ <li>Parsing of Dbref and DbxRef feature types as database
+ references</li>
+ <li>URL links generated from description line for
+ regular-expression based URL links (applet and application)
+ <li>Non-positional feature URL links are shown in link menu</li>
+ <li>Linked viewing of nucleic acid sequences and structures</li>
+ <li>Automatic Scrolling option in View menu to display the
+ currently highlighted region of an alignment.</li>
+ <li>Optionally scale multi-character column labels to fit within each column<!-- todo for applet --></li>
+ <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
+ </ul>
+ <em>Vamsas Capabilities</em>
+ <ul>
+ <li>
+ <li>Improved VAMSAS synchronization (jalview archive used to
+ preserve views, structures, and tree display settings)</li>
+ <li>Import of vamsas documents from disk or URL via command line</li>
+ <li>Sharing of selected regions between views and with other
+ VAMSAS applications (Experimental feature!)</li>
+ <li>Updated API to VAMSAS version 0.2</li>
+ </ul>
+ <em>Application</em>
+ <ul>
+ <li>New hidden columns and rows and representatives capabilities
+ in annotations file (in progress - not yet fully implemented)</li>
+ <li>Order an alignment in order of average feature score or
+ total feature count</li>
+ <li>Shading features by score or associated description</li>
+ <li>Group-associated automatic and user-defined alignment
+ annotation</li>
+ <li>Symbol distributions for each column can be exported and
+ visualized as sequence logos</li>
+ <li>Optional automatic sort of associated alignment view when a
+ new tree is opened.</li>
+ <li>Jalview Java Console</li>
+ </ul>
+ <em>Applet</em>
+ <ul>
+ <li>Middle button resizes annotation row height</li>
+ <li>parameter to enable automatic sort of associated alignment view when a
+ new tree is opened.</li>
+ <li>Non-positional features displayed in sequence ID tooltip</li>
+ </ul>
+ <em>Other</em>
+ <ul>
+ <li>Features format: graduated colour definitions and
+ specification of feature scores</li>
+ <li>
+ </td>
+ <td>
+ <ul>
+ <li>Source field in GFF files parsed as feature source rather
+ than description</li>
+ <li>URL links generated for all feature links (bugfix)</li>
+ <li>Added URL embedding instructions to features file
+ documentation.</li>
+ <li>Codons containing ambiguous nucleotides translated as 'X' in
+ peptide product</li>
+ <li>Match case switch in find dialog box works for both sequence
+ ID and sequence string and query strings do not have to be in upper
+ case to match case-insensitively.</li>
+ <li>AMSA files only contain first column of multi-character column annotation labels</li>
+ <li>PDB files without embedded PDB IDs given a friendly name</li>
+ <li>Applet:
+ <ul>
+ <li></li>
+ </ul>
+ </li>
+ <li>Application:
+ <ul>
+ <li>Better handling of exceptions during sequence retrieval</li>
+ <li>Dasobert generated non-positional feature URL link text
+ excludes the start_end suffix (application)</li>
+ <li>PDB files retrieved from URLs are cached properly</li>
+ <li>Sequence description lines properly shared via VAMSAS</li>
+ <li>Sequence fetcher fetches multiple records for all data
+ sources</li>
+ <li>Ensured that command line das feature retrieval completes
+ before alignment figures are generated.</li>
+ </ul>
+ </li>