</ul>
</li>
<li>Jmol integration updated to Jmol v14.2.14</li>
- <li>Import and export of Jalview alignment views as <a href="">BioJSON</a></li>
+ <li>Import and export of Jalview alignment views as <a
+ href="">BioJSON</a></li>
<li>New alignment annotation file statements for
reference sequences and marking hidden columns</li>
- <li>Assign an alignment reference sequence to highlight
- variation</li>
+ <li>Reference sequence based alignment shading to
+ highlight variation</li>
<li>Select or hide columns according to alignment
annotation</li>
- <li>Find option for locating sequences by
- description</li>
+ <li>Find option for locating sequences by description</li>
<li>Conserved physicochemical properties shown in amino
acid conservation row</li>
<li>Alignments can be sorted by number of RNA helices</li>
- </ul>
- <em>Application</em>
+ </ul> <em>Application</em>
<ul>
- <li>Optional embedding of BioJSON data when exporting
- alignment figures to HTML</li>
- <li>New Export Settings dialog to control hidden region
- export in flat file generation</li>
<li>New cDNA/Protein analysis capabilities
<ul>
<li>Get Cross-References should open a Split Frame
</li>
<li>Use REST API to talk to Chimera</li>
- <li>Selected regions in Chimera are highlighted in linked Jalview windows</li>
-
- <li>Calculate UPGMA and NJ trees using sequence feature
- similarity</li>
+ <li>Selected regions in Chimera are highlighted in linked
+ Jalview windows</li>
<li>VARNA RNA viewer updated to v3.93</li>
- <li>VARNA views are saved in Jalview
- Projects</li>
- <li>Pseudoknots displayed as Jalview RNA annotation can be shown in VARNA</li>
-
- <li>changed 'View nucleotide structure' submenu to 'View VARNA 2D Structure'</li>
- <li>change "View protein structure" menu option to "3D Structure ..."</li>
+ <li>VARNA views are saved in Jalview Projects</li>
+ <li>Pseudoknots displayed as Jalview RNA annotation can
+ be shown in VARNA</li>
<li>Make groups for selection uses marked columns as well
as the active selected region</li>
- <li>allow different similarity matrix calculations for
- tree building and PCA</li>
+ <li>Calculate UPGMA and NJ trees using sequence feature
+ similarity</li>
+ <li>New Export options
+ <ul>
+ <li>New Export Settings dialog to control hidden
+ region export in flat file generation</li>
- <li>Export alignment views for display with the <a
- href="http://biojs.io/d/msa">BioJS MSAViewer</a></li>
-
- <li>Export scrollable SVG in HTML page</li>
+ <li>Export alignment views for display with the <a
+ href="http://biojs.io/d/msa">BioJS MSAViewer</a></li>
- <li>Interactive free text and structured queries with the
- PDBe Search API for PDB data retrieval</li>
- <li>PDBe Search API based discovery and selection of PDB structures to
- view for a sequence set</li>
+ <li>Export scrollable SVG in HTML page</li>
+ <li>Optional embedding of BioJSON data when exporting
+ alignment figures to HTML</li>
+ </li>
+ <li>3D structure retrieval and display
+ <ul>
+ <li>Free text and structured queries with
+ the PDBe Search API</li>
+ <li>PDBe Search API based discovery and selection of
+ PDB structures for a sequence set</li>
+ </ul>
+ </li>
<li>JPred4 employed for protein secondary structure
predictions</li>
<li>Hide Insertions menu option to hide unaligned columns
for one or a group of sequences</li>
- <li>Automatically hide insertions in alignments imported from the JPred4 web server</li>
+ <li>Automatically hide insertions in alignments imported
+ from the JPred4 web server</li>
<li>(Nearly) Native 'Quaqua' dialogs for browsing file
system on OSX<br />LGPL libraries courtesy of <a
href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
</li>
+ <li>changed 'View nucleotide structure' submenu to 'View
+ VARNA 2D Structure'</li>
+ <li>change "View protein structure" menu option to "3D
+ Structure ..."</li>
+
</ul> <em>Applet</em>
<ul>
- <li>New parameters to enable SplitFrame view (file2, scaleProteinAsCdna)</li>
+ <li>New layout for applet example pages</li>
+ <li>New parameters to enable SplitFrame view (file2,enableSplitFrame,
+ scaleProteinAsCdna)</li>
<li>New example demonstrating linked viewing of cDNA and
Protein alignments</li>
- <li>New layout for applet example pages</li>
- </ul>
- <em>Development and deployment</em>
+ </ul> <em>Development and deployment</em>
+ <ul>
<li>Java 1.7 minimum requirement for Jalview 2.9</li>
<li>Include installation type and git revision in build
properties and console log output</li>
- <li>Github project and web URL for storing BioJsMSA
- Templates</li>
- <li>Jalview's unit tests now managed with TestNG</li></td>
+ <li>Jalview Github organisation, and new github site for
+ storing BioJsMSA Templates</li>
+ <li>Jalview's unit tests now managed with TestNG</li></ul></td>
<td>
<!-- <em>General</em>
<ul>
git://source.jalview.org / jalview.git / blobdiff