</td>
<td>
<ul>
- <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>
+ <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>Subdivide alignment and groups based on identity of selected subsequence (Make Groups from Selection).</li>
+ <li>New hide/show options including Shift+Control+H to hide everything but the currently selected region.</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>
</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>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>DAS Dbref and DbxRef feature types are parsed as database
+ references and protein_name is parsed as description line (BioSapiens terms).</li>
+ <li>Enable or disable non-positional feature and database
+ references in sequence ID tooltip from View menu in application.</li>
+ <!-- <li>New hidden columns and rows and representatives capabilities
+ in annotations file (in progress - not yet fully implemented)</li> -->
+ <li>Group-associated consensus, sequence logos and conservation plots</li>
<li>Symbol distributions for each column can be exported and
visualized as sequence logos</li>
+ <li>Optionally scale multi-character column labels to fit within each column of annotation row<!-- todo for applet --></li>
<li>Optional automatic sort of associated alignment view when a
new tree is opened.</li>
<li>Jalview Java Console</li>
<li>New preference items for sequence ID tooltip and consensus annotation</li>
+ <li>Client to submit sequences and IDs to <a href="webServices/index.html#envision2">Envision2</a> Workflows</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>
+ <li>New Parameters
+ <ul>
+ <li>sortByTree (true/false) - automatically sort the associated alignment view by the tree when a new tree is opened.</li>
+ <li>showTreeBootstraps (true/false) - show or hide branch bootstraps (default is to show them if available)</li>
+ <li>showTreeDistances (true/false) - show or hide branch lengths (default is to show them if available)</li>
+ <li>showUnlinkedTreeNodes (true/false) - indicate if unassociated nodes should be highlighted in the tree view</li>
+ <li>heightScale and widthScale (1.0 or more) - increase the height or width of a cell in the alignment grid relative to the current font size.</li>
+ </ul>
+ </li>
+ <li>Non-positional features displayed in sequence ID tooltip</li>
+ <li></li>
</ul>
<em>Other</em>
<ul>
<li>Features format: graduated colour definitions and
specification of feature scores</li>
+ <li>Alignment Annotations format: new keywords for group associated annotation (GROUP_REF) and annotation row display properties (ROW_PROPERTIES)</li>
<li>XML formats extended to support graduated feature colourschemes, group associated annotation, and profile visualization settings.</li>
</td>
<td>
<ul>
<li>Source field in GFF files parsed as feature source rather
than description</li>
+ <li>Non-positional features are now included in sequence feature and gff files (controlled via non-positional feature visibility in tooltip).</li>
<li>URL links generated for all feature links (bugfix)</li>
<li>Added URL embedding instructions to features file
documentation.</li>
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>Jalview Annotation File generation/parsing consistent with documentation (e.g. Stockholm annotation can be exported and re-imported)</li>
<li>PDB files without embedded PDB IDs given a friendly name</li>
+ <li>Find incrementally searches ID string matches as well as subsequence matches, and correctly reports total number of both.</li>
<li>Applet:
<ul>
<li></li>
sources</li>
<li>Ensured that command line das feature retrieval completes
before alignment figures are generated.</li>
+ <li>Reduced time taken when opening file browser for first time.</li>
</ul>
</li>
</ul>
git://source.jalview.org / jalview.git / blobdiff