[Jalview-announce] Jalview 2.2

Mon Nov 20 15:28:25 GMT 2006

Hello to all Jalview users,

This is a pre-release message to let you know that we are hoping to 
release the next version of Jalview early next week.

Jalview 2.2 has had several optimizations made to the code to allow 
usable editing and hiding of sequences of large alignments (~5000 
protein sequences). Also the undo/redo system has been reimplemented to 
be much more memory efficient than previous Jalview releases.

New features include:

* Multiple views of a sequence set - edits are linked between (tabbed) 
windows, but each view can be coloured differently, may have different 
sequence regions hidden etc.
* Easily add, amend, delete sequence features
* Reload alignment from File or URL
* Save implemented as well as existing Save As
* Set the text colour (can be thresholded on background colour, eg white 
on a dark background, black on a light background colour.)
* Right align sequence ids
* Set colour of lower case residues in a user defined colour scheme
* General Menu reordering and Menu item accelerator keys added - Watch 
out, Paste with Control-V now pastes to the active window, you must use 
Control-Shift-V to paste sequences to a new window!

Features resolved:
* 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
* Feature descriptions can display < and > tags if <html> is not used, 
or with &lt; &gt; if description specified within <html> tags.
* Zoom working in PCA viewer
* Sequence Descriptions retained after running a web service