--- /dev/null
+---
+channel: release
+version: 2.10.0
+date: 2016-10-06
+---
+
+## New Features
+
+
+
+### General
+- <!-- JAL-2124 --> Updated Spanish translations.
+- <!-- JAL-2164,JAL-1919,JAL-2148 --> Jmol now primary parser for importing structure data to Jalview. Enables mmCIF and better PDB parsing.
+- <!-- JAL-192 ---> Alignment ruler shows positions relative to reference sequence
+- <!-- JAL-2202 --> Position/residue shown in status bar when mousing over sequence associated annotation
+- <!-- JAL-2171 --> Default RNA SS symbol to 'matching bracket' for manual entry
+- <!-- JAL-2214 --> RNA Structure consensus indicates wc-only '()', canonical '[]' and invalid '{}' base pair populations for each column
+- <!-- JAL-2092 --> Feature settings popup menu options for showing or hiding columns containing a feature
+- <!-- JAL-1557 --> Edit selected group by double clicking on group and sequence associated annotation labels
+- <!-- JAL-2236 --> Sequence name added to annotation label in select/hide columns by annotation and colour by annotation dialogs
+
+
+### Application
+- <!-- JAL-2050--> Automatically hide introns when opening a gene/transcript view
+- <!-- JAL-1563 --> Uniprot Sequence fetcher Free Text Search dialog
+- <!-- JAL-1957, JAL-1479 JAL-1491 --> UniProt - PDB protein structure mappings with the EMBL-EBI PDBe SIFTS database
+- <!-- JAL-2079 --> Updated download sites used for Rfam and Pfam sources to xfam.org
+- <!-- JAL-2084 --> Disabled Rfam(Full) in the sequence fetcher
+- <!-- JAL-2123 --> Show residue labels in Chimera when mousing over sequences in Jalview
+- <!-- JAL-2027--> Support for reverse-complement coding regions in ENA and EMBL
+- <!-- JAL-1855, JAL-2113, JAL-2114--> Upgrade to EMBL XML 1.2 for record retrieval via ENA rest API
+- <!-- JAL-2027 --> Support for ENA CDS records with reverse complement operator
+- <!-- JAL-1812 --> Update to groovy-2.4.6-indy - for faster groovy script execution
+- <!-- JAL-1812 --> New 'execute Groovy script' option in an alignment window's Calculate menu
+- <!-- JAL-1812 --> Allow groovy scripts that call Jalview.getAlignFrames() to run in headless mode
+- <!-- JAL-2068 --> Support for creating new alignment calculation workers from groovy scripts
+- <!-- JAL-1369 ---> Store/restore reference sequence in Jalview projects
+- <!-- JAL-1803 --> Chain codes for a sequence's PDB associations are now saved/restored from project
+- <!-- JAL-1993 --> Database selection dialog always shown before sequence fetcher is opened
+- <!-- JAL-2183 --> Double click on an entry in Jalview's database chooser opens a sequence fetcher
+- <!-- JAL-1563 --> Free-text search client for UniProt using the UniProt REST API
+- <!-- JAL-2168 --> -nonews command line parameter to prevent the news reader opening
+- <!-- JAL-2028 --> Displayed columns for PDBe and Uniprot querying stored in preferences
+- <!-- JAL-2091 --> Pagination for displaying PDBe and Uniprot search results
+- <!-- JAL-1977--> Tooltips shown on database chooser
+- <!-- JAL-391 --> Reverse complement function in calculate menu for nucleotide sequences
+- <!-- JAL-2005, JAL-599 --> Alignment sort by feature scores and feature counts preserves alignment ordering (and debugged for complex feature sets).
+- <!-- JAL-2152--> Chimera 1.11.1 minimum requirement for viewing structures with Jalview 2.10
+- <!-- 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
+- <!-- JAL-2049 --> Protein sequence variant annotation computed for 'sequence_variant' annotation on CDS regions (Ensembl)
+- <!-- JAL-2232 --> ENA CDS 'show cross references' for Uniprot sequences
+- <!-- JAL-2213,JAL-1856 --> Improved warning messages when DB Ref Fetcher fails to match, or otherwise updates sequence data from external database records.
+- <!-- JAL-2154 --> Revised Jalview Project format for efficient recovery of sequence coding and alignment annotation relationships.
+
+
+## Issues Resolved
+
+
+
+### General
+ - <!-- JAL-2077 --> reinstate CTRL-click for opening pop-up menu on OSX
+ - <!-- JAL-2018--> Export features in Jalview format (again) includes graduated colourschemes
+ - <!-- JAL-2172,JAL-1722, JAL-2001--> More responsive when working with big alignments and lots of hidden columns
+ - <!-- JAL-2053--> Hidden column markers not always rendered at right of alignment window
+ - <!-- JAL-2067 --> Tidied up links in help file table of contents
+ - <!-- JAL-2072 --> Feature based tree calculation not shown for DNA alignments
+ - <!-- JAL-2075 --> Hidden columns ignored during feature based tree calculation
+ - <!-- JAL-2065 --> Alignment view stops updating when show unconserved enabled for group on alignment
+ - <!-- JAL-2086 --> Cannot insert gaps into sequence when set as reference
+ - <!-- JAL-2146 --> Alignment column in status incorrectly shown as "Sequence position" when mousing over annotation
+ - <!-- JAL-2099 --> Incorrect column numbers in ruler when hidden columns present
+ - <!-- JAL-1577 --> Colour by RNA Helices not enabled when user created annotation added to alignment
+ - <!-- JAL-1841 --> RNA Structure consensus only computed for '()' base pair annotation
+ - <!-- JAL-2215, JAL-1841 --> Enabling 'Ignore Gaps' results in zero scores for all base pairs in RNA Structure Consensus
+ - <!-- JAL-2174--> Extend selection with columns containing feature not working
+ - <!-- JAL-2275 --> Pfam format writer puts extra space at beginning of sequence
+ - <!-- JAL-1827 --> Incomplete sequence extracted from pdb entry 3a6s
+ - <!-- JAL-2238 --> Cannot create groups on an alignment from from a tree when t-coffee scores are shown
+ - <!-- JAL-1836,1967 --> Cannot import and view PDB structures with chains containing negative resnums (4q4h)
+ - <!-- JAL-1998 --> ArithmeticExceptions raised when parsing some structures
+ - <!-- JAL-1991, JAl-1952 --> 'Empty' alignment blocks added to Clustal, PIR and PileUp output
+ - <!-- JAL-2008 --> Reordering sequence features that are not visible causes alignment window to repaint
+ - <!-- 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
+ - <!-- JAL-1797 --> amino acid physicochemical conservation calculation should be case independent
+ - <!-- JAL-2173 --> Remove annotation also updates hidden columns
+ - <!-- 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)
+ - <!-- JAL-2065 --> Null pointer exceptions and redraw problems when reference sequence defined and 'show non-conserved' enabled
+ - <!-- JAL-1306 --> Quality and Conservation are now shown on load even when Consensus calculation is disabled
+ - <!-- JAL-1932 --> Remove right on penultimate column of alignment does nothing
+
+
+### Application
+ - <!-- JAL-1552--> URLs and links can't be imported by drag'n'drop on OSX when launched via webstart (note - not yet fixed for El Capitan)
+ - <!-- JAL-1911--> Corrupt preferences for SVG, EPS & HTML output when running on non-gb/us i18n platforms
+ - <!-- JAL-1944 --> Error thrown when exporting a view with hidden sequences as flat-file alignment
+ - <!-- JAL-2030--> InstallAnywhere distribution fails when launching Chimera
+ - <!-- JAL-2080--> Jalview very slow to launch via webstart (also hotfix for 2.9.0b2)
+ - <!-- JAL-2085 --> Cannot save project when view has a reference sequence defined
+ - <!-- JAL-1011 --> Columns are suddenly selected in other alignments and views when revealing hidden columns
+ - <!-- JAL-1989 --> Hide columns not mirrored in complement view in a cDNA/Protein splitframe
+ - <!-- JAL-1369 --> Cannot save/restore representative sequence from project when only one sequence is represented
+ - <!-- JAL-2002 --> Disabled 'Best Uniprot Coverage' option in Structure Chooser
+ - <!-- JAL-2215 --> Modifying 'Ignore Gaps' on consensus or structure consensus didn't refresh annotation panel
+ - <!-- JAL-1962 --> View mapping in structure view shows mappings between sequence and all chains in a PDB file
+ - <!-- JAL-2102, JAL-2101, JAL-2102, --> PDB and Uniprot FTS dialogs format columns correctly, don't display array data, sort columns according to type
+ - <!-- JAL-1975 --> Export complete shown after destination file chooser is cancelled during an image export
+ - <!-- JAL-2025 --> Error when querying PDB Service with sequence name containing special characters
+ - <!-- JAL-2024 --> Manual PDB structure querying should be case insensitive
+ - <!-- JAL-2104 --> Large tooltips with broken HTML formatting don't wrap
+ - <!-- JAL-1128 --> Figures exported from wrapped view are truncated so L looks like I in consensus annotation
+ - <!-- JAL-2003 --> Export features should only export the currently displayed features for the current selection or view
+ - <!-- JAL-2036 --> Enable 'Get Cross-References' in menu after fetching cross-references, and restoring from project
+ - <!-- JAL-2032 --> Mouseover of a copy of a sequence is not followed in the structure viewer
+ - <!-- JAL-2163 --> Titles for individual alignments in splitframe not restored from project
+ - <!-- JAL-2145 --> missing autocalculated annotation at trailing end of protein alignment in transcript/product splitview when pad-gaps not enabled by default
+ - <!-- JAL-1797 --> amino acid physicochemical conservation is case dependent
+ - <!-- JAL-1448 --> RSS reader doesn't stay hidden after last article has been read (reopened issue due to internationalisation problems)
+ - <!-- JAL-1960 --> Only offer PDB structures in structure viewer based on sequence name, PDB and UniProt cross-references
+ - <!-- JAL-1976 --> No progress bar shown during export of alignment as HTML
+ - <!-- JAL-2213 --> Structures not always superimposed after multiple structures are shown for one or more sequences.
+ - <!-- JAL-1370 --> Reference sequence characters should not be replaced with '.' when 'Show unconserved' format option is enabled.
+ - <!-- JAL-1823 --> Cannot specify chain code when entering specific PDB id for sequence
+ - <!-- JAL-1944 --> File->Export->.. as doesn't work when 'Export hidden sequences' is enabled, but 'export hidden columns' is disabled.
+ - <!--JAL-2026--> Best Quality option in structure chooser selects lowest rather than highest resolution structures for each sequence
+ - <!-- JAL-1887 --> Incorrect start and end reported for PDB to sequence mapping in 'View Mappings' report
+ - <!-- JAL-2284 --> Unable to read old Jalview projects that contain non-XML data added after Jalvew wrote project.
+ - <!-- JAL-2118 --> Newly created annotation row reorders after clicking on it to create new annotation for a column.
+ - <!-- JAL-1980 --> Null Pointer Exception raised when pressing Add on an orphaned cut'n'paste window.
+
+
+### Applet
+ - <!-- JAL-2151 --> Incorrect columns are selected when hidden columns present before start of sequence
+ - <!-- JAL-1986 --> Missing dependencies on applet pages (JSON jars)
+ - <!-- JAL-1947 --> Overview pixel size changes when sequences are hidden in applet
+ - <!-- JAL-1996 --> Updated instructions for applet deployment on examples pages.