+ <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-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 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---></li>
+ </ul></td>
+ <td>
+ <div align="left">
+ <em>General</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-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 -->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>
+ <li><!-- JAL-2099 -->Incorrect column numbers in ruler when hidden columns present</li>
+ <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>
+ <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-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>
+ <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-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>
+ </tr>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
+ <em>16/10/2015</em></strong>
+ </div>
+ </td>
+ <td><em>General</em>
+ <ul>
+ <li>Time stamps for signed Jalview application and applet
+ jars</li>
+ </ul></td>
+ <td>
+ <div align="left">
+ <em>Application</em>
+ <ul>
+ <li>Duplicate group consensus and conservation rows
+ shown when tree is partitioned</li>
+ <li>Erratic behaviour when tree partitions made with
+ multiple cDNA/Protein split views</li>
+ </ul>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
+ <em>8/10/2015</em></strong>
+ </div>
+ </td>
+ <td><em>General</em>
+ <ul>
+ <li>Updated Spanish translations of localized text for
+ 2.9</li>
+ </ul> <em>Application</em>
+ <ul>
+ <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
+ <li>Signed OSX InstallAnywhere installer<br></li>
+ <li>Support for per-sequence based annotations in BioJSON</li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>Split frame example added to applet examples page</li>
+ </ul></td>
+ <td>
+ <div align="left">
+ <em>General</em>
+ <ul>
+ <li>Mapping of cDNA to protein in split frames
+ incorrect when sequence start > 1</li>
+ <li>Broken images in filter column by annotation dialog
+ documentation</li>
+ <li>Feature colours not parsed from features file</li>
+ <li>Exceptions and incomplete link URLs recovered when
+ loading a features file containing HTML tags in feature
+ description</li>
+
+ </ul>
+ <em>Application</em>
+ <ul>
+ <li>Annotations corrupted after BioJS export and
+ reimport</li>
+ <li>Incorrect sequence limits after Fetch DB References
+ with 'trim retrieved sequences'</li>
+ <li>Incorrect warning about deleting all data when
+ deleting selected columns</li>
+ <li>Patch to build system for shipping properly signed
+ JNLP templates for webstart launch</li>
+ <li>EMBL-PDBe fetcher/viewer dialogs do not offer
+ unreleased structures for download or viewing</li>
+ <li>Tab/space/return keystroke operation of EMBL-PDBe
+ fetcher/viewer dialogs works correctly</li>
+ <li>Disabled 'minimise' button on Jalview windows
+ running on OSX to workaround redraw hang bug</li>
+ <li>Split cDNA/Protein view position and geometry not
+ recovered from jalview project</li>
+ <li>Initial enabled/disabled state of annotation menu
+ sorter 'show autocalculated first/last' corresponds to
+ alignment view</li>
+ <li>Restoring of Clustal, RNA Helices and T-Coffee
+ color schemes from BioJSON</li>
+ </ul>
+ <em>Applet</em>
+ <ul>
+ <li>Reorder sequences mirrored in cDNA/Protein split
+ frame</li>
+ <li>Applet with Jmol examples not loading correctly</li>
+ </ul>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td><div align="center">
+ <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
+ </div></td>
+ <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>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="features/bioJsonFormat.html">BioJSON</a></li>
+ <li>New alignment annotation file statements for
+ reference sequences and marking hidden columns</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>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>
+ <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>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>Make groups for selection uses marked columns as well
+ as the active selected region</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://msa.biojs.net/">BioJS MSAViewer</a></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>(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 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>
+ </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>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>
+ </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>Consensus RNA secondary secondary structure
+ predictions are not highlighted in amber</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
+ width checkbox not enabled</li>
+ <li>Stopped a warning dialog from being shown when
+ creating user defined colours</li>
+ <li>'View Mapping' in structure viewer shows sequence
+ mappings for just that viewer's sequences</li>
+ <li>Workaround for superposing PDB files containing
+ multiple models in Chimera</li>
+ <li>Report sequence position in status bar when hovering
+ over Jmol structure</li>
+ <li>Cannot output gaps as '.' symbols with Selection ->
+ output to text box</li>
+ <li>Flat file exports of alignments with hidden columns
+ have incorrect sequence start/end</li>
+ <li>'Aligning' a second chain to a Chimera structure from
+ Jalview fails</li>
+ <li>Colour schemes applied to structure viewers don't
+ work for nucleotide</li>
+ <li>Loading/cut'n'pasting an empty or invalid file leads
+ 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 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 in
+ console if Chimera has been opened</li>
+ <li>Mouseover to Chimera not working</li>
+ <li>Miscellaneous ENA XML feature qualifiers not
+ retrieved</li>
+ <li>NPE in annotation renderer after 'Extract Scores'</li>
+ <li>If two structures in one Chimera window, mouseover of
+ 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
+ in right place after 'view flanking regions'</li>
+ <li>File Save As type unset when current file format is
+ unknown</li>
+ <li>Save as '.jar' option removed for saving Jalview
+ projects</li>
+ <li>Colour by Sequence colouring in Chimera more
+ responsive</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>Jalview's tooltip wraps long texts containing no
+ spaces</li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>Jmol to JalviewLite mouseover/link not working</li>
+ <li>JalviewLite can't import sequences with ID
+ descriptions containing angle brackets</li>
+ </ul> <em>General</em>