What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=d1d141d30b133f0a400e7fb369ebe9cce029c4d5;hb=898cc5eb4089b2dcf8605e5e2c33387879cd3389;hp=bd57b81b2859697831859af7babf8ebab04729d5;hpb=b5edbd2a03d16372bc3e8019ddbf3840dcfe38ed;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index bd57b81..d1d141d 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,30 +1,78 @@ - -What's new ? - -

What's new ?

Jalview Version 2.07

Sequence Fetcher has been added to quickly - retrieve sequences with known ids from several databases.

Sequence Features enhanced to allow - the user to display all features of a Uniprot file on the alignment and subsequently - colour, hide or show overlapping features.

Choose to omit /start-end from sequences when - saving files. This is important for saving files to be used by some programs - which cannot read the original Jalview sequence output with the appended /start-end.

PDB structure viewer enhanced. Mapping - between sequence and structure has been enhanced, colours on the alignment are - reflected in the structure viewer.

Jalview Applet can read - in feature files, PDB files be used as input to HTML form See the website - to find out the new parameters available for the Applet Version of Jalview.

Issues Resolved

Group Editing is possible with Control and mouse click. Alt key and mouse press - does not work as this translates as the middle mouse button, which since 2.04 - is now used to scroll the alignment and change the font size.

HTML export now writes groups and features which were previously missing.

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 $DB_ACCESSION$. +

+ +