X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=0382f2225f7b83d424b1b6b660b6eef0c7673e3f;hb=33342a9ee15da4873f9fd94bc2330bc73e7bc51f;hp=1c2088579ed5e6c1ff6426efcdcc65b30092e996;hpb=7585bdc21653bdb66d604ed5efa95497f28c7eb5;p=jalview.git
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- What's new in Jalview 2.10.1 ?
+ What's new in Jalview 2.10.3b1 ?
- Jalview 2.10.1 was released on 24th 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.
+ This release - Jalview 2.10.3b1 is the January 2018 patch release for Version 2.10.3 was released in November 2017. The major focus was to
+ improve Jalview's sequence features datamodel and the scalability of
+ the alignment rendering system. The bugs fixed in this release can be found in the 2.10.3b1
+ Release Notes.
+
+ The highlights for Jalview 2.10.3 include:
- - 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.
+ - Faster and more responsive UI when importing and working
+ with wide alignments and handling hundreds and thousands of
+ sequence features
+ - Improved usability with PDB and UniProt Free Text
+ Search dialog, and new tab for retrieval of sequences for lists of
+ IDs.
+
+ - Short names assigned to sequences retrieved from UniProt
+ - Groovy console upgraded to 2.4.12 (improved support for Java 9)
-
- 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 $DB_ACCESSION$.
+ Experimental Features
+
+
+ Remember, please enable the Experimental Features option in
+ the Jalview Desktop's Tools menu, and then restart Jalview
+ if you want to try out features below:
+
+