X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=4dfc54e201bb54ba3074ac62ae61e29135f9e099;hb=f2450b343be28d1b46f71a809d3d85041bf5aa62;hp=1f2b22147b646b85a20b3342032dcdcc9344c818;hpb=c02981a7d326f468c33f39f84992a0b183009121;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 1f2b221..4dfc54e 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -24,73 +24,34 @@

- 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, and RNA secondary structure + annotation.

New UI, and faster and more configurable - implementation for PCA, Neighbour-Joining and UPGMA Trees
- Menu entries for calculating PCA and different types of tree have - been replaced by a single Calculations dialog box. The - underlying implementation for the PCA and tree calculations have - been made faster and more memory efficient. A new framework has - also been created for the score models used to calculate distances - between sequences. This framework allows import of substitution - matrices in NCBI and AAIndex format, and custom score models to be - created via a groovy script.
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. +
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 -

- 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. -

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.

- Scripting
New groovy examples - demonstrate Jalview 2.10.2 APIs for creation of data-driven - colourschemes, and custom alignment file handlers. The FeatureAnnotationWorker - introduced in Jalview 2.10 has also been refactored to allow - efficient counting across multiple feature types. Please be aware - that feature counter scripts created for earlier versions will not - execute in Jalview 2.10.2. -

+ The full list of bugs fixed in this release can be found in the 2.10.5 Release Notes. The majority of improvement 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 do this !

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. The 'Save As' dialog for + Jalview's Groovy Console remains affected - we hope to address this + in the next major release.