X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=4dfc54e201bb54ba3074ac62ae61e29135f9e099;hb=0e575263043797b2e9bbd74386cd5851c09433af;hp=1c2088579ed5e6c1ff6426efcdcc65b30092e996;hpb=7585bdc21653bdb66d604ed5efa95497f28c7eb5;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 1c20885..4dfc54e 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -24,55 +24,34 @@

- What's new in Jalview 2.10.1 ? -

- Jalview 2.10.1 was released on 24th 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. + What's new in Jalview 2.10.5 ?

Jalview 2.10.5 is a minor release that includes critical + patches for users working with Ensembl, and RNA secondary structure + annotation.

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. +
EPS, PNG and SVG export now includes hidden sequence + markers, and representative sequences are marked in bold.
Ensembl Client updated for Ensembl Rest API v7.
The + latest Ensembl API is not backwards compatible with earlier + versions of Jalview, so if you require Ensembl functionality you + will need to install this release. +
Improved support for VIENNA extended dot-bracket notation + for RNA secondary structure
Positional and selected region highlighting in VARNA + 'trimmed sequence' view now more reliable

- 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 $DB_ACCESSION$. -

+ The full list of bugs fixed in this release can be found in the 2.10.5 Release Notes. The majority of improvement in 2.10.5 are due to Jalview users + contacting us via the jalview-discuss email list. Thanks to everyone + who took the time to do this !

Jalview and Java 10

This release addresses a critical bug for OSX users who are + running Jalview with Java 10 which can prevent files being saved + correctly through the 'Save As' dialog box. The 'Save As' dialog for + Jalview's Groovy Console remains affected - we hope to address this + in the next major release.