<td><em>General</em>
<ul>
<li>Linked visualisation and analysis of DNA and Protein
- alignments:<ul>
- <li>Translated cDNA alignments shown as split protein and
- DNA alignment views</li>
- <li>Codon consensus annotation for linked protein and
- cDNA alignment views</li>
- <li>Add cDNA or Protein product sequences to Protein or
- cDNA alignments</li>
- <li>Reconstruct linked cDNA alignment from aligned
- protein sequences</i>
- </ul></li>
-
- <li>Update Jmol to v14.2n</li>
-
- <li>BioJSON data exchange</li>
-
+ alignments:
+ <ul>
+ <li>Translated cDNA alignments shown as split protein
+ and DNA alignment views</li>
+ <li>Codon consensus annotation for linked protein and
+ cDNA alignment views</li>
+ <li>Link cDNA or Protein product sequences by loading
+ them onto Protein or cDNA alignments</li>
+ <li>Reconstruct linked cDNA alignment from aligned
+ protein sequences</li>
+ </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>New alignment annotation file statements for
reference sequences and marking hidden columns</li>
-
- <li>Alignments can be sorted by number of RNA helices</li>
-
- <li>Assign a reference sequence to highlight
- variation and consensus analysis</li>
-
+ <li>Assign an alignment reference sequence to highlight
+ variation</li>
<li>Select or hide columns according to alignment
annotation</li>
<li>Find option for locating sequences by
description</li>
-
<li>Conserved physicochemical properties shown in amino
acid conservation row</li>
-
- </ul> <em>Application</em>
+ <li>Alignments can be sorted by number of RNA helices</li>
+ </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 view
- with cDNA/Protein</li>
- <li>Detect when nucleotide sequences and protein
- sequences are placed in the same alignment</li>
- <li>Split cDNA/Protein views are saved in Jalview
- projects</li>
- <li>support '*' in amino acid sequences to indicate stop
- codon</li>
- </ul></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
+ view with cDNA/Protein</li>
+ <li>Detect when nucleotide sequences and protein
+ sequences are placed in the same alignment</li>
+ <li>Split cDNA/Protein views are saved in Jalview
+ projects</li>
+ </ul>
+ </li>
<li>Use REST API to talk to Chimera</li>
<li>Selected regions in Chimera are highlighted in linked Jalview windows</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>change "View protein structure" menu option to "3D Structure ..."</li>
<li>Make groups for selection uses marked columns as well
as the active selected region</li>
tree building and PCA</li>
<li>Export alignment views for display with the <a
- href="">BioJS MSAViewer</a></li>
- <li>Scrollable SVG for HTML export</li>
+ href="http://biojs.io/d/msa">BioJS MSAViewer</a></li>
+
+ <li>Export scrollable SVG in HTML page</li>
- <li>Novel data discovery and retrieval mechanism using
- PDBe Search API</li>
- <li>Smarter technique for selecting PDB structures to
- view in Jalview</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>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>(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>
</ul> <em>Applet</em>
<ul>
- <li>Parameter to enable SplitFrame view</li>? check other
- parameters in applet ?
+ <li>New parameters to enable SplitFrame view (file2, scaleProteinAsCdna)</li>
<li>New example demonstrating linked viewing of cDNA and
Protein alignments</li>
<li>New layout for applet example pages</li>
<li>Github project and web URL for storing BioJsMSA
Templates</li>
<li>Jalview's unit tests now managed with TestNG</li></td>
- <td><em>General</em>
+ <td>
+ <!-- <em>General</em>
<ul>
- </ul> <!-- issues resolved --> <em>Application</em>
+ </ul> -->
+ <!-- issues resolved --> <em>Application</em>
<ul>
<li>Escape should close any open find dialogs</li>
- <li>typo in select-by-features status report</li>
+ <li>Typo in select-by-features status report</li>
<li>Consensus RNA secondary secondary structure
predictions are not highlighted in amber</li>
- <li>missing gap character means v2.7 example file appears
- unaligned REVIEW</li>
+ <li>Missing gap character in v2.7 example file means
+ alignment appears unaligned when pad-gaps is not enabled</li>
<li>First switch to RNA Helices colouring doesn't colour
associated structure views</li>
<li>ID width preference option is greyed out when auto
to a grey/invisible alignment window</li>
<li>Exported Jpred annotation from a sequence region
imports to different position</li>
- <li>Space at beginning of sequence feature mouseover
- tooltip on some platforms</li>
+ <li>Space at beginning of sequence feature tooltips shown
+ on some platforms</li>
<li>Chimera viewer 'View | Show Chain' menu is not
populated</li>
- <li>'New View' fails with a Null Pointer Exception if
- Chimera has been opened</li>
+ <li>'New View' fails with a Null Pointer Exception in
+ console if Chimera has been opened</li>
<li>Mouseover to Chimera not working</li>
<li>Miscellaneous ENA XML feature qualifiers not
retrieved</li>
either sequence shows on first structure</li>
<li>'Show annotations' options should not make
non-positional annotations visible</li>
- <li>subsequence secondary structure annotation not shown
+ <li>Subsequence secondary structure annotation not shown
in right place after 'view flanking regions'</li>
<li>File Save As type unset when current file format is
unknown</li>
- <li>Native 'Quaqua' dialogs for saving and loading files
- on OSX</li>
<li>Save as '.jar' option removed for saving Jalview
projects</li>
<li>Colour by Sequence colouring in Chimera more
responsive</li>
- <li>Can disable consensus calculation independently of
- quality and conservation</li>
<li>Cannot 'add reference annotation' for a sequence in
several views on same alignment</li>
<li>Cannot show linked products for EMBL / ENA records</li>
<li>Nucleotide ambiguity codes involving R not recognised</li>
</ul> <em>Deployment and Documentation</em>
<ul>
-
+ <li>Applet example pages appear different to the rest of
+ www.jalview.org</li>
</ul> <em>Application Known issues</em>
<ul>
<li>Incomplete sequence extracted from PDB entry 3a6s</li>
placed above or below non-autocalculated rows</li>
<li>Jalview dekstop becomes sluggish at full screen in
ultra-high resolution</li>
+ <li>Cannot disable consensus calculation independently of
+ quality and conservation</li>
+ <li>Mouseover highlighting between cDNA and protein can
+ become sluggish with more than one splitframe shown</li>
</ul> <em>Applet Known Issues</em>
<ul>
<li>Core PDB parsing code requires Jmol</li>
<li>Sequence canvas panel goes white when alignment
window is being resized
<li>
- </ul></td>
+ </ul>
+ </td>
</tr>
<tr>
<td width="60" nowrap>
git://source.jalview.org / jalview.git / commitdiff