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+
What's new ?
-What's new ?
+
+ What's new in Jalview 2.10.1 ?
+
+
+ Jalview 2.10.1 was released on 29th November 2016. Full details are
+ in the Jalview 2.10.1
+ Release Notes, but the highlights are below. This is also the
+ first release to include contributions from Kira Mourão, who
+ joined Jalview's core development team in October 2016.
+
+
+ - More memory efficient
We've slimmed
+ down the consensus analysis data structures used by Jalview so
+ even wider alignments can be worked with.
+ - Select highlighted region
Press 'B'
+ or use the new menu option in the alignment window's Select menu
+ to mark columns containing highlighted regions generated from
+ structure selections, mouse-overs, or resulting from a Find
+ operation.
+ - New custom link mechanism for opening URLs
+ for database cross references.
If you have customised URL
+ links in your Jalview preferences, then you may already have seen
+ the warning dialog (see below).
+ - New command line export option for BioJS
+ MSAviewer
A number of small bugs with the HTML export
+ functions from the Jalview desktop were also fixed.
+ - Small but significant changes to the
+ physicochemical properties and consensus calculations
Threonine
+ is no longer considered a non-hydrophobic residue in the protein
+ conservation calculation, and minor bugs addressed in PID and
+ consensus colouring.
+ - Correct display of disulphide bond
+ features
In linked structure views, Jalview would
+ highlight all residues between in addition to the two linked
+ cysteines. The 'select columns by feature' function in the feature
+ settings would also select all intermediate columns.
+
-Jalview Version 2.3
-Jmol 11 integration
-PDB views in Jalview XML
-Slide sequences
-Edit sequence in place
-EMBL CDS features
-DAS Feature mapping
-Feature ordering
-Alignment Properties
-Annotation Scores
-Sort by scores
-Feature/annotation editing in applet
-
-
-Issues Resolved
-
-Headless state operation in 2.2.1
-
Incorrect and unstable DNA pairwise alignment
-
-Cut and paste of sequences with annotation
-
-Feature group display state in XML
-Feature ordering in XML
-2.2.1 applet had no feature transparency
-
-
-See the Release History page for
-details of all new features and resolved issues.
+
+ Warning dialog about updating
+ your configured URL links
In the desktop prior to Jalview
+ 2.10.1, the only way to configure custom links for a particular
+ database cross-reference for a sequence was to give it a name that exactly
+ matched the database source, and a regular expression for filtering
+ out any spurious matches generated when the custom linked was tested
+ against the Sequence's ID string. Since the introduction of the
+ $DB_ACCESSION$ token, however, $SEQUENCE_ID$ will not be used for
+ database cross-reference accession strings, and if you have custom
+ links configured, Jalview will raise a warning message so let you
+ know that you may need to update your links to use $DB_ACCESSION$.
+