</head>
<body>
<p>
- <strong>What's new in Jalview 2.10.1 ?</strong>
+ <strong>What's new in Jalview 2.10.2 ?</strong>
</p>
<p>
- Jalview 2.10.1 was released on 29th November 2016. Full details are
- in the <a href="releases.html#Jalview.2.10.1">Jalview 2.10.1
- Release Notes</a>, 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.
+ Full details about Jalview 2.10.2 are in the <a
+ href="releases.html#Jalview.2.10.2"> Release Notes</a>, but the
+ highlights are below.
</p>
<ul>
- <li><strong>More memory efficient</strong><br />We've slimmed
- down the consensus analysis data structures used by Jalview so
- even wider alignments can be worked with.</li>
- <li><strong>Select highlighted region</strong><br />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.</li>
- <li><strong>New custom link mechanism for opening URLs
- for database cross references.</strong><br /> If you have customised URL
- links in your Jalview preferences, then you may already have seen
- the <a href="#warning"> warning dialog (see below).</a></li>
- <li><strong>New command line export option for BioJS
- MSAviewer</strong><br />A number of small bugs with the HTML export
- functions from the Jalview desktop were also fixed.</li>
- <li><strong>Small but significant changes to the
- physicochemical properties and consensus calculations</strong><br />Threonine
- is no longer considered a non-hydrophobic residue in the protein
- conservation calculation, and minor bugs addressed in PID and
- consensus colouring.</li>
- <li><strong>Correct display of disulphide bond
- features</strong><br /> 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.
+ <li><strong>Update to JABAWS 2.2</strong><br />Jalview's
+ alignment, protein conservation analysis, and protein disorder and
+ RNA secondary structure prediction services are now provided by <a
+ href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS 2.2</a>.
+ Several of the programs provided as services have been updated, so
+ their options and parameters have changed.</li>
+ <li>New preferences for <a href="webServices/urllinks.html">opening
+ web pages for database cross-references</a> via the UK Elixir's
+ EMBL-EBI's MIRIAM database and identifiers.org services.
+ </li>
+ <li><em>Showing and hiding regions</em>
+ <ul>
+ <li><a href="menus/popupMenu.html#hideinserts">Hide
+ insertions</a> in the PopUp menu has changed its behaviour.
+ Prior to 2.10.2, columns were only shown or hidden according
+ to gaps in the sequence under the popup menu. Now, only
+ columns that are gapped in all selected sequences as well as
+ the sequence under the popup menu are hidden, and column
+ visibility outside the selected region is left as is. This
+ makes it easy to filter insertions from the alignment view
+ (just select the region containing insertions to remove)
+ without affecting the rest of the hidden columns.</li>
+ </ul></li>
</ul>
-
<p>
- <strong><a name="warning">Warning dialog about updating
- your configured URL links</a></strong><br /> 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 <em>exactly</em>
- 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 $DB_ACCESSION$.
+ <strong><a name="experimental">Experimental Features</a></strong>
</p>
+ <p>
+ This release of Jalview includes a new option in the Jalview Desktop
+ that allows you to try out features that are still in development.
+ To access the features described below, please first enable the <strong>Tools→Enable
+ Experimental Features</strong> option, and then restart Jalview.
+ </p>
+ <ul>
+ <li><em>Annotation transfer between Chimera and Jalview</em><br />Two
+ <a href="features/chimera.html#experimental">new entries in
+ the Chimera viewer's Chimera menu</a> allow positional annotation to
+ be exchanged between Chimera and Jalview.</li>
+ </ul>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff