X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=d1d141d30b133f0a400e7fb369ebe9cce029c4d5;hb=8018887d2917a478af88ab5ed3c7621d7cf18967;hp=e453b5d8c20072a93cfcdec8de2c8413a4af9ad9;hpb=b46d87ba6875733cb9baf59e9391dcd69d4c0419;p=jalview.git
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-
-What's new
-
-What's new
-If you can read this then you'll already have seen some of the recent changes
- made to Jalview.
- Jalview takes advantage of some of the more recent user interface developments
- in the Java programming language. For instance Jalview is now a multi windowed
- application, this keeps all your Jalview windows neatly together in one main
- application window.
-If you were familiar with the original Jalview, here is a list of important
- features you should know about the current development:
-
- - Editing sequences is no longer the default when mouse clicking the alignment.
- Instead, mouse clicking on the alignment will create a "selection region"
- which may be full sequences or groups of residues.
- - To edit a sequence, the "Shift" key must be held down
- - To edit groups, either the "Alt" key or the "Control"
- key must be held down.
- - Colours maybe applied to the background, ie the whole alignment, or to selected
- regions. If the tickbox "Apply colour to all groups" is ticked (this
- is the defualt), then the colour will be applied to all groups.
- - Use the right mouse button (apple and click on the mac) to define a selected
- region on the alignment as a new group.
- - Conservation is automatically updated whenever the alignment is edited
- - There is no "quick draw" option
- - Edits can be undone! (and redone)
-
-
-
+
+
+
+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 $DB_ACCESSION$.
+
+
+