X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2FwhatsNew.html;h=3538ff4b1738f95e0516332b803c139306ed7206;hb=56ac68efa74c060e03a2b5b805ca8b8872f907e1;hp=1c2088579ed5e6c1ff6426efcdcc65b30092e996;hpb=7585bdc21653bdb66d604ed5efa95497f28c7eb5;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 1c20885..3538ff4 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -24,55 +24,48 @@

- 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. + Jalview 2.11 - major and minor new features

Jalview 2.11 introduces support for loading VCF files, and new + filters and shading models for sequence features. Under the hood, + we've addressed many bugs, and also made some important changes in + the way the Jalview desktop is installed and launched.

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. +
VCF Support. Proteins and genomic contigs with + chromosomal location annotation (such as protein coding genes + retrieved from Ensembl) can be annotated with variants imported + from a local VCF file.
The Jalview Launcher and Update System
+ Jalview's new installation model means you'll only need to + download and install Jalview once. After installation, Jalview + will automatically keep itself up to date. The launcher also sets + Jalview's memory automatically, so you'll never again have to + manually configure Java's memory settings.
We are grateful to + Install4J who provided us with a free license for their + installation system, and Jalview's over the air update system is + via Getdown.

- 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 2.11 Release Notes. +

+ Jalview and Java 11, 13, and onwards

Java 11 provides improved performance and better OS + integration, so we now recommend users select our Java 11 Jalview + distribution rather than the legacy Java 8 build.

+ Known Issues - update for 211 +

OSX: The 'Open File' dialog for Jalview's Groovy Console + appears with the title 'Save As', and attempting to select a file + to load yields a FileNotFound exception.
The workaround is to first + clear the 'Untitled' filename before selecting the file you wish + to load. +
OSX: Links don't open when clicked on or via the Sequence + or Alignment window popup menu.
OSX (Webstart): JalviewÂ only displays old news feed items