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<div align="center">
- <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>27/9/2016</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>
<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-2050-->Automatically hide introns when opening a gene/transcript view</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-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2 for record retrieval via ENA rest API</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-1993 -->Database selection dialog always shown before sequence fetcher is opened</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>
+ <li><!-- JAL-391 -->Reverse complement function in calculate menu for nucleotide sequences</li>
+ <li>
+ <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores and feature counts preserves alignment ordering (and debugged for complex feature sets).
+ </li>
+ <li>
+ <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for viewing structures with Jalview 2.10
+ </li>
+ <li>
+ <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve genome, transcript CCDS and gene ids via the Ensembl and Ensembl Genomes REST API
+ </li>
+ <li>
+ <!-- JAL-2049 -->Protein sequence variant annotation computed for 'sequence_variant' annotation on CDS regions (Ensembl)
+ </li>
+ <li><!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot sequences</li>
+ <li>
+ <!-- JAL- -->
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
</ul> <em>Applet</em>
<ul>
<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-2172,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-2067 -->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-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-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>
+ <li><!-- JAL-2008 -->Reordering sequence features that are not visible causes alignment window to repaint</li>
+ <li>
+ <!-- JAL-2006 -->Threshold sliders don't work in
+ graduated colour and colour by annotation row for e-value
+ scores associated with features and annotation rows
+ </li>
+ <li>
+ <!-- JAL-1797 -->amino acid physicochemical conservation
+ calculation should be case independent
+ </li>
+ <li>
+ <!-- JAL-2173 -->Remove annotation also updates hidden
+ columns
+ </li>
+ <li>
+ <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in example file (uniref50.fa, feredoxin.fa, unaligned.fa, exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
+ </li>
+ <li>
+ <!-- JAL-2065 -->Null pointer exceptions and redraw problems when reference sequence defined and 'show non-conserved' enabled
+ </li>
+ <li><!-- JAL-1306 -->Quality and Conservation are now shown on load even when Consensus calculation is disabled</li>
+ <li>
+ <!-- -->
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
</ul>
<em>Application</em>
<ul>
<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-1962 -->View mapping in structure view shows mappings between sequence and all chains in a PDB file</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>
+ <li><!-- JAL-2003 -->Export features should only export the currently displayed features for the current selection or view</li>
+ <li><!-- JAL-2036 -->Enable 'Get Cross-References' in menu after fetching cross-references</li>
+ <li><!-- JAL-2032 -->Mouseover of a copy of a sequence is not followed in the structure viewer</li>
+ <li><!-- JAL-2163 -->Titles for individual alignments in splitframe not restored from project</li>
+ <li>
+ <!-- JAL-2145 -->missing autocalculated annotation at trailing end of protein alignment in transcript/product splitview when pad-gaps not enabled by default
+ </li>
+ <li>
+ <!-- JAL-1797 -->amino acid physicochemical conservation is case dependent
+ </li>
+ <li>
+ <!-- JAL-1448 -->RSS reader doesn't stay hidden after last article has been read (reopened issue due to internationalisation problems)
+ </li>
+ <li><!-- JAL-1960 -->Only offer PDB structures in structure viewer based on sequence name, PDB and Uniprot cross-references</li>
+
+ <li>
+ <!-- JAL-1976 -->No progress bar shown during export of alignment as HTML
+ </li>
+ <li>
+ <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB Ref Fetcher fails to match, or otherwise updates sequence data from external database records.
+ </li>
+ <li>
+ <!-- JAL-2213 -->Structures not always superimposed after multiple structures are shown for one or more sequences.
+ </li>
+ <li>
+ <!-- JAL-1370 -->Reference sequence characters should not be replaced with '.' when 'Show unconserved' format option is enabled.
+ </li>
+ <li>
+ <!-- JAL-1823 -->Cannot specify chain code when entering specific PDB id for sequence
+ </li>
+ <li>
+ <!-- JAL-1944 -->File->Export->.. as doesn't work when 'Export hidden sequences' is enabled, but 'export hidden columns' is disabled.
+ </li>
+ <li><!--JAL-2026-->Best Quality option in structure chooser selects lowest rather than highest resolution structures for each sequence</li>
+ <li>
+ <!-- JAL-1887 -->Incorrect start and end reported for PDB to sequence mapping in 'View Mappings' report
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
+ <li>
+ <!-- JAL- -->
+ </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><!-- JAL-2151 -->Incorrect columns are selected when hidden columns present before start of sequence</li>
+ <li><!-- JAL-1986 -->Missing dependencies on applet pages (JSON jars)</li>
+ <li>
+ <!-- JAL-1947 -->Overview pixel size changes when sequences are hidden in applet
+ </li>
+ <li><!-- JAL-1996 -->Updated instructions for applet deployment on examples pages.
+ </li>
</ul>
</div>
</td>
git://source.jalview.org / jalview.git / blobdiff