What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=d1d141d30b133f0a400e7fb369ebe9cce029c4d5;hb=47fd498a6fe7d2e3350a9e87c526bf1e59d00be5;hp=8c28564b88fd535421d6938c6ca2bad0311930d2;hpb=7cdae57d68efc9bae8e64511bd7d41eda7d6c33d;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 8c28564..d1d141d 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,34 +1,78 @@ - -What's new ? - -

What's new ?

Jalview Version 2.08

Editing can be locked to the selection area. - Any edits made within the locked area do not affect the rest of the alignment.

Keyboard editing - press F2 to toggle cursor mode On / Off. For a full list - of keyboard controls, look here.

Create sequence features from searches. - Previously results from searches were added as alignment positions, which was - wrong. Now the search results are saved as sequence features and their visibility - and colour can be modified using the Sequence - Feature Settings window.

Precalculated annotations can be loaded onto alignments. The Annotation - File format is a tab delimited set of values.

Features file allows grouping of - features. The Sequence Feature Settings - window then makes it very easy to set the visibility of groups of features. -

Annotation Colouring - scheme added. A new colour scheme which colours columns on a per-column value.

Smooth fonts off by default - faster rendering. Toggle on / off from the View - menu, or can be set in Preferences.

Choose to toggle Autocalculate Consensus On/Off from the Calculate menu.
-

Issues Resolved

Drag & Drop fixed on Linux

Jalview Archive file faster to load/save, sequence descriptions saved.
-

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 $DB_ACCESSION$. +

+ +