<tr>
<td width="60" nowrap>
<div align="center">
- <strong><a name="Jalview.2.9.1">2.9.1</a><br /> <em>1/6/2016</em></strong>
+ <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>20/9/2016</em></strong>
</div>
</td>
<td><em>General</em>
<ul>
- <li></li>
+ <li><!-- JAL-2164,JAL-1919,-->Jmol now primary parser for importing structure data to Jalview. Enables mmCIF and better PDB parsing.</li>
+ <li><!-- JAL-192 --->Alignment ruler shows positions relative to reference sequence</li>
+ <li><!-- JAL-2202 -->Position/residue shown in status bar when mousing over sequence associated annotation</li>
</ul> <em>Application</em>
<ul>
- <li></li>
+ <li><!-- JAL---></li>
+ <li><!-- JAL---></li>
+ <li><!-- JAL---></li>
+ <li><!-- JAL---></li>
+ <li><!-- JAL---></li>
+ <li><!-- JAL---></li>
+ <li><!-- JAL-2123 -->Show residue labels in Chimera when mousing over sequences in Jalview</li>
+ <li><!-- JAL-2027-->Support for reverse-complement coding regions in ENA and EMBL</li>
+ <li><!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2 for ENA record retrieval</li>
+ <li><!-- JAL 1812 -->New 'execute Groovy script' option in an alignment window's Calculate menu</li>
+ <li><!-- JAL 1812 -->Allow groovy scripts that call Jalview.getAlignFrames() to run in headless mode</li>
+ <li><!-- JAL-1369 --->Store/restore reference sequence in Jalview projects</li>
+ <li><!-- JAL-1803-->Chain codes for a sequence's PDB associations are now saved/restored from project</li>
+ <li><!-- JAL-2183-->Double click on an entry in Jalview's database chooser opens a sequence fetcher</li>
+ <li><!-- JAL-2183-->Free-text search client for UniProt using the UniProt web API</li>
+
+
</ul> <em>Applet</em>
<ul>
- <li></li>
+ <li><!-- JAL---></li>
</ul></td>
<td>
<div align="left">
<em>General</em>
<ul>
- <li></li>
+ <li><!-- JAL-2077 -->reinstate CTRL-click for opening pop-up menu on OSX</li>
+ <li><!-- JAL-2018-->Export features in Jalview format (again) includes graduated colourschemes</li>
+ <li><!-- JAL-1722, JAL-2001-->More responsive when working with big alignments and lots of hidden columns</li>
+ <li><!-- JAL-2053-->hidden column markers not always rendered at right of alignment window</li>
+ <li><!-- JAL-2067, JAL- -->Tidied up links in help file table of contents</li>
+ <li><!-- JAL-2072 -->Feature based tree calculation not shown for DNA alignments</li>
+ <li><!-- JAL-2075 -->Hidden columns ignored during feature based tree calculation</li>
+ <li><!-- JAL-2065 -->Alignment view stops updating when show unconserved enabled for group on alignment</li>
+ <li><!-- JAL-2086 -->Cannot insert gaps into sequence when set as reference</li>
+ <li><!-- JAL-2146 -->Alignment column in status incorrectly shown as "Sequence position" when mousing over annotation</li>
+
</ul>
<em>Application</em>
<ul>
- <li></li>
+ <li><!-- JAL-1944 not yet fixed Error thrown when exporting a view with hidden sequences as flat-file alignment--></li>
+ <li><!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML output when running on non-gb/us i18n platforms</li>
+ <li><!-- JAL-1552-->URLs and links can imported by drag'n'drop on OSX webstart</li>
+ <li><!-- JAL-2030-->InstallAnywhere distribution fails when launching Chimera</li>
+ <li><!-- JAL-2080-->Jalview very slow to launch via webstart (also hotfix for 2.9.0b2)</li>
+ <li><!-- JAL-2085 -->Cannot save project when view has a reference sequence defined</li>
+ <li><!-- JAL-1011 -->Columns are suddenly selected in other alignments and views when revealing hidden columns</li>
+ <li><!-- JAL-1989 -->Hide columns not mirrored in complement view in a cDNA/Protein splitframe</li>
+ <li><!-- JAL-1369 -->Cannot save/restore representative sequence from project when only one sequence is represented</li>
+
+ <!-- may exclude, this is an external service stability issue JAL-1941 /> RNA 3D structure not added via DSSR service</li> -->
</ul>
<em>Applet</em>
<ul>
- <li></li>
+ <li><!-- --></li>
</ul>
</div>
</td>
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>
+ href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
<li>Export scrollable SVG in HTML page</li>
<li>Optional embedding of BioJSON data when exporting
<a href="https://www.certum.eu">Certum</a> to the Jalview
open source project).
</li>
- <li>Jalview SRS links replaced by Uniprot and EBI-search
+ <li>Jalview SRS links replaced by UniProt and EBI-search
</li>
<li>Output in Stockholm format</li>
<li>Allow import of data from gzipped files</li>
current built in colourscheme is saved as new scheme</li>
<li>AlignFrame->Save in application pops up save
dialog for valid filename/format</li>
- <li>Cannot view associated structure for Uniprot sequence</li>
- <li>PDB file association breaks for Uniprot sequence
+ <li>Cannot view associated structure for UniProt sequence</li>
+ <li>PDB file association breaks for UniProt sequence
P37173</li>
<li>Associate PDB from file dialog does not tell you
which sequence is to be associated with the file</li>
between different screens.</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>
+ <li>Client to submit sequences and IDs to Envision2 Workflows</li>
<li><em>Vamsas Capabilities</em>
<ul>
<li>Improved VAMSAS synchronization (Jalview archive
<li>Save works when Jalview project is default format</li>
<li>Save as dialog opened if current alignment format is
not a valid output format</li>
- <li>Uniprot canonical names introduced for both das and
+ <li>UniProt canonical names introduced for both das and
vamsas</li>
<li>Histidine should be midblue (not pink!) in Zappo</li>
<li>error messages passed up and output when data read
due to null pointer exceptions</li>
<li>Secondary structure lines are drawn starting from
first column of alignment</li>
- <li>Uniprot XML import updated for new schema release in
+ <li>UniProt XML import updated for new schema release in
July 2008</li>
<li>Sequence feature to sequence ID match for Features
file is case-insensitive</li>
<li>Re-instated Zoom function for PCA
<li>Sequence descriptions conserved in web service
analysis results
- <li>Uniprot ID discoverer uses any word separated by
+ <li>UniProt ID discoverer uses any word separated by
∣
<li>WsDbFetch query/result association resolved
<li>Tree leaf to sequence mapping improved
git://source.jalview.org / jalview.git / blobdiff