What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2FwhatsNew.html;h=d1d141d30b133f0a400e7fb369ebe9cce029c4d5;hb=e4a8b62decc8ca3d448389539464a0897b465343;hp=5bb50f9eb0e177707442c3bc1fd76fad58414dc2;hpb=20bddfcf8ef1a53bce455b7599f8066b8ccba0d4;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 5bb50f9..d1d141d 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,28 +1,78 @@ - -What's new ? - -

What's new ?

Jalview Version 2.1

The multiple sequence alignment program MAFFT - is available from the default Web Service list.

The sequence feature retrieval system using DBFetch from EBI has been replaced - with DAS Feature fetching capabilities.

Hide sequences and columns

Export Annotations and Features

GFF file reading / writing

Associate structures with sequences from local PDB files

Add sequences to exisiting alignment

Recently opened files / URL lists

Applet can launch the full application

Applet has transparency for features (Java 1.2 required)

Applet has user defined colours parameter

Issues Resolved

Redundancy Panel reinstalled in the Applet

Monospaced font - EPS / rescaling bug fixed

Annotation files with sequence references bug fixed

See the Release History page for details of all - new features and resolved issues.

- - + + + +What's new ? + + +

+ 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 $DB_ACCESSION$. +

+ +