<tr>
<td width="60" nowrap>
<div align="center">
- <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>20/9/2016</em></strong>
+ <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>04/10/2016</em></strong>
</div>
</td>
<td><em>General</em>
<ul>
- <li><!-- JAL-2164,JAL-1919,-->Jmol now primary parser for importing structure data to Jalview. Enables mmCIF and better PDB parsing.</li>
+ <li><!-- JAL-2164,JAL-1919,JAL-2148 -->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>
<li><!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket' for manual entry</li>
<li><!-- JAL-2214 -->RNA Structure consensus indicates wc-only '()', canonical '[]' and invalid '{}' base pair populations for each column</li>
+ <li><!-- JAL-2092 -->Feature settings popup menu options for showing or hiding columns containing a feature</li>
+ <li><!-- JAL-1557 -->Edit selected group by double clicking on group and sequence associated annotation labels</li>
+ <li><!-- JAL-2236 -->Sequence name added to annotation label in select/hide columns by annotation and colour by annotation dialogs</li>
</ul> <em>Application</em>
<ul>
<li><!-- JAL---></li>
<li><!-- JAL---></li>
- <li><!-- JAL---></li>
- <li><!-- JAL---></li>
- <li><!-- JAL---></li>
+ <li><!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search dialog</li>
+ <li><!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein structure mappings with the EMBL-EBI PDBe SIFTS database</li>
<li><!-- JAL-2079 -->Updated download sites used for Rfam and Pfam sources to xfam.org</li>
<li><!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher</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-2027 -->Support for ENA CDS records with reverse complement operator</li>
+ <li><!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster groovy script execution</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-2068 -->Support for creating new alignment calculation workers from groovy scripts</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-1563-->Free-text search client for UniProt using the UniProt REST API</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-1563 -->Free-text search client for UniProt using the UniProt REST API</li>
+ <li><!-- JAL-2168 -->-nonews command line parameter to prevent the news reader opening</li>
+ <li><!-- JAL-2028 -->Displayed columns for PDBe and Uniprot querying stored in preferences</li>
+ <li><!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot search results</li>
+ <li><!-- JAL-1977-->Tooltips shown on database chooser</li>
+
</ul> <em>Applet</em>
<ul>
<li><!-- JAL-1577 -->Colour by RNA Helices not enabled when user created annotation added to alignment</li>
<li><!-- JAL-1841 -->RNA Structure consensus only computed for '()' base pair annotation</li>
<li><!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results in zero scores for all base pairs in RNA Structure Consensus</li>
-
+ <li><!-- JAL-2174-->Extend selection with columns containing feature not working</li>
+ <li><!-- JAL-2275 -->Pfam format writer puts extra space at beginning of sequence</li>
+ <li><!-- JAL-1827 -->Incomplete sequence extracted from pdb entry 3a6s </li>
+ <li><!-- JAL-2238 -->Cannot create groups on an alignment from from a tree when t-coffee scores are shown</li>
+ <li><!-- JAL-1836,1967 -->Cannot import and view PDB structures with chains containing negative resnums (4q4h)</li>
+ <li><!-- JAL-1998 -->ArithmeticExceptions raised when parsing some structures</li>
+ <li><!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added to Clustal, PIR and PileUp output</li>
</ul>
<em>Application</em>
<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>
<li><!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option in Structure Chooser</li>
- <li><!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or structure consensus didn't refresh annotation panel</li>
+ <li><!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or structure consensus didn't refresh annotation panel</li>
+ <li><!-- JAL-1962 -->View mapping in structure view shows mappings between sequence and all chains in a PDB file</li>
+ <li><!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS dialogs format columns correctly, don't display array data, sort columns according to type</li>
+ <li><!-- JAL-1975 -->Export complete shown after destination file chooser is cancelled during an image export </li>
+ <li><!-- JAL-2025 -->Error when querying PDB Service with sequence name containing special characters</li>
+ <li><!-- JAL-2024 -->Manual PDB structure querying should be case insensitive</li>
+ <li><!-- JAL-2104 -->Large tooltips with broken HTML formatting don't wrap</li>
+ <li><!-- JAL-1128 -->Figures exported from wrapped view are truncated so L looks like I in consensus annotation</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><!-- JAL-2151 -->Incorrect columns are selected when hidden columns present before start of sequence</li>
</ul>
</div>
</td>
git://source.jalview.org / jalview.git / blobdiff