X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=4b821794e06755ef60c7a2421b4b3faee15327d3;hb=4a9a2fc8a1b1a66b21e66429083f27a6fc8541b9;hp=d1d141d30b133f0a400e7fb369ebe9cce029c4d5;hpb=898cc5eb4089b2dcf8605e5e2c33387879cd3389;p=jalview.git
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- What's new in Jalview 2.10.1 ?
+ What's new in Jalview 2.10.2 ?
- 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.
+ Full details about Jalview 2.10.2 are in the Release Notes, but the
+ highlights are below.
- - 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.
+ - Update to JABAWS 2.2
Jalview's
+ alignment, protein conservation analysis, and protein disorder and
+ RNA secondary structure prediction services are now provided by JABAWS 2.2.
+ Several of the programs provided as services have been updated, so
+ their options and parameters have changed.
+ - New preferences for opening
+ web pages for database cross-references via the UK Elixir's
+ EMBL-EBI's MIRIAM database and identifiers.org services.
+
+ - Showing and hiding regions
+
+ - Hide
+ insertions in the PopUp menu has changed its behaviour.
+ Prior to 2.10.2, columns were only shown or hidden according
+ to gaps in the sequence under the popup menu. Now, only
+ columns that are gapped in all selected sequences as well as
+ the sequence under the popup menu are hidden, and column
+ visibility outside the selected region is left as is. This
+ makes it easy to filter insertions from the alignment view
+ (just select the region containing insertions to remove)
+ without affecting the rest of the hidden 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 $DB_ACCESSION$.
+ Experimental Features
+
+ This release of Jalview includes a new option in the Jalview Desktop
+ that allows you to try out features that are still in development.
+ To access the features described below, please first enable the Tools→Enable
+ Experimental Features option, and then restart Jalview.
+
+