What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=d1d141d30b133f0a400e7fb369ebe9cce029c4d5;hb=14a3cc9277d30d14bec559a12d9af72bd2955aff;hp=344c322233d893da5d0fd96edbcb175d510b5380;hpb=85fb1c79fd82d7eada801624f745635632be8362;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 344c322..d1d141d 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,54 +1,78 @@ -What's new ? + + +What's new ? + -

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. +

Jalview Version 2.2

Multiple views with different styles, colours, hidden regions for one alignment -

Easily add, amend and delete sequence features -

"Reload" alignment from File or URL to revert to original -

"Save" to current filename or "Save As" to new filename -

Set different text colour for dark or light background -

Right align sequence ids -

Set colour of lower case residues in a user defined colour scheme -

Menu Rearrangements: New Format for alignment layout and Select for region selection. -

Menu item accelerator keys added -

Control-V pastes sequences to active window, Control-Shift-V pastes to a new window. -

Raise/Minimise alignment and all associated windows from desktop window's window menu -

Select and colour whole branches of a tree

'New Window' button on the 'Output to Text box' alignment output -option to open a new alignment window after editing.

Issues Resolved

-Optimisations for large alignments: faster multithreaded calculations and Undo/Redo system. -

Remove empty columns - if empty columns exist at the end of the -alignment bug fixed. -

DAS feature fetching slowed down, doesn't overload DAS servers -

DAS feature fetching can be cancelled -

Correct display of > and < symbols for feature descriptions without explicit <html> tags. -

Zoom working in PCA viewer -

Sequence Descriptions retained after running a web service -

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

+ 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 $DB_ACCESSION$. +