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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
What's new ?
-
- What's new ?
-
-
- The Jalview 2.7 release features new web services, and important
- improvements to the way in which Jalview handles alignments and
- associated PDB structures, as well as numerous minor improvements and
- bug fixes. Version 2.7 of the JalviewLite applet also features a
- significantly enhanced Javascript API enabling it to be more easily
- integrated with javascript based web applications.
For full
- details see the Jalview 2.7
- release history.
-
-
- Highlights in Jalview Desktop Version 2.7
-
-
+
+ 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.
+
-
- Issues Resolved (a select list - see the release history for full details)
-
-
-
- Issues in the Jalview Desktop
-
- - Problems viewing associated structures for sequences
- retrieved from UNIPROT
- - Problems viewing Jalview projects from older versions in
- version 2.6
- - Preservation of hidden annotation rows and tree bootstrap
- values in projects
- - Newly added JABAWS servers not always visible in web services
- menu
-
- Issues specific to the JalviewLite Applet
-
- - Layout problems when lots of annotation rows are displayed
- - <= shown as = in annotation row tooltip
- - export features raises exception when no features exist
- - relative URLs not handled properly when used in parameters
- and annotation files
-
- Issues affecting both applet and application
-
- - sequence numbering not preserved in MSF alignment output
- - sequence associated secondary structure not correctly parsed
- in interleaved stockholm
- - sequences containing lowercase letters are not properly
- associated with their pdb files
- - Jalview PDB file reader does not extract sequence from deoxy
- nucleotide chains correctly
- - Sequence length given in alignment properties window is off
- by 1
-
+
+ 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 $DB_ACCESSION$.
+