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What's new ?
-
- What's new ?
Jalview 2.8.0b1 is a bugfix
- release for Jalview version 2.8.
As usual you can find the
- highlights below, and the comprehensive list is given in the Jalview 2.8.0b1 Release Notes.
-
- This bug fix release includes numerous minor enhancements made over
- the last 12 months. Importantly, it is also the first release that
- provides Jalview as a trusted application, signed with a certificate
- donated to us by Certum.
+ 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.
+
+
+
+ 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 $DB_ACCESSION$.
- Enhancements and new features
-
- - Allow disorder predictions to be made on the current
- selection (or visible selection) in the same way that JPred works
- - allow import of data from gzipped files
- - Improved per-sequence 'colour-by-annotation' performance
- - Support '' style escaping of quotes in Newick files
- - group options for JABAWS service by command line name
- - Select primary source when selecting authority in database
- fetcher GUI
- - COMBINE statement uses current SEQUENCE_REF and GROUP_REF
- scope to group annotation rows
- - add .mfa to FASTA file extensions recognised by Jalview
- - groovy scripting for headless jalview operation
- - Output in Stockholm format
-
- Bug fixes
-
- - Uniprot and PDB database cross-reference fetching works
- properly
- - 'View all structures' in the desktop is more reliable
- - Web services parameter dialog box shows the options enabled
- for different presets
- - Interactive creation of RNA secondary structure works more
- smoothly
- - Keyboard mode 'P' command jumps to the right place
- - Improved support for parsing database cross-references via
- Stockholm and Rfam database
- - Improved semantics in annotation files for grouping
- annotation rows associated with particular sequences and groups
- - More robust DNA->Amino acid translation
- - Improved Headless-mode operation for DAS annotation
- retrieval, groovy script execution and alignment figure generation
- - annotation label tooltip text needs to be wrapped
-