- <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-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-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-2154 -->Revised Jalview Project format for
+ efficient recovery of sequence coding and alignment
+ annotation relationships.
+ </li>
+ </ul> <!-- <em>Applet</em>
+ <ul>
+ <li>
+ -- JAL---
+ </li>
+ </ul> --></td>
+ <td>
+ <div align="left">
+ <em>General</em>
+ <ul>