X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=866cfc3e4fb667bbffc75f72dc10c939bbc6c7d2;hb=7b52727e20e0d9bf798b5ded667d5bd6cb1c0397;hp=4b821794e06755ef60c7a2421b4b3faee15327d3;hpb=91daa39be6c29713a821318497ff347a0569a52a;p=jalview.git
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- What's new in Jalview 2.10.2 ?
-
-
- Full details about Jalview 2.10.2 are in the Release Notes, but the
- highlights are below.
+ What's new in Jalview 2.10.5 ?
+ Jalview 2.10.5 is a minor release that includes critical
+ patches for users working with Ensembl, RNA secondary structure
+ annotation, and those running Jalview on OSX with Java 10.
- - Update to JABAWS 2.2
Jalview's
- alignment, protein conservation analysis, and protein disorder and
- RNA secondary structure prediction services are now provided by JABAWS 2.2.
- Several of the programs provided as services have been updated, so
- their options and parameters have changed.
- - New preferences for opening
- web pages for database cross-references via the UK Elixir's
- EMBL-EBI's MIRIAM database and identifiers.org services.
+
- Jalview's default memory limit increased to 1G. If you have
+ problems starting Jalview 2.10.5 and you have 1G or less
+ physical memory on your machine, you will need to reduce the memory allocated to
+ Jalview.
+
+ - EPS, PNG and SVG export now includes hidden sequence
+ markers, and representative sequences are marked in bold.
+ - Ensembl Client updated for Ensembl Rest API v7.
The
+ latest Ensembl API is not backwards compatible with earlier
+ versions of Jalview, so if you require Ensembl functionality you
+ will need to install this release.
- - Showing and hiding regions
-
- - Hide
- insertions 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.
-
+ - Improved support for VIENNA extended dot-bracket notation
+ for RNA secondary structure
+ - Positional and selected region highlighting in VARNA
+ 'trimmed sequence' view now more reliable
- Experimental Features
+ The full list of bugs fixed in this release can be found in the 2.10.5 Release Notes. The
+ majority of bug fixes and improvements in 2.10.5 are due to Jalview users
+ contacting us via the jalview-discuss email list. Thanks to everyone
+ who took the time to help make Jalview better !
- 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 Tools→Enable
- Experimental Features option, and then restart Jalview.
+ Jalview and Java 10
+ This release addresses a critical bug for OSX users who are
+ running Jalview with Java 10 which can prevent files being saved
+ correctly through the 'Save As' dialog box.
+ Known Issues
- - Annotation transfer between Chimera and Jalview
Two
- new entries in
- the Chimera viewer's Chimera menu allow positional annotation to
- be exchanged between Chimera and Jalview.
+ - OSX: The 'Open File' dialog for Jalview's Groovy Console
+ appears with the title 'Save As', and attempting to select a file to load yields a FileNotFound exception.The workaround is to first clear the 'Untitled' filename before selecting the file you wish to load.
+
+ - OSX: Links don't open when clicked on or via the Sequence or Alignment window popup menu.
+ - OSX (Webstart): Jalview only displays old news feed items