What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=4dfc54e201bb54ba3074ac62ae61e29135f9e099;hb=0e575263043797b2e9bbd74386cd5851c09433af;hp=88e8ee9114fe5b7fe723e4d17d314de97798dbfa;hpb=c78133920a45e1b5b0b1bea5807f3ae880425914;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 88e8ee9..4dfc54e 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,103 +1,57 @@ + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> What's new ? -

- What's new ? -

- The Jalview 2.7 release features new web services, and important - improvements to the way in which Jalview handles alignments and - associated PDB structures, as well as numerous minor improvements and - bug fixes. Version 2.7 of the JalviewLite applet also features a - significantly enhanced Javascript API enabling it to be more easily - integrated with javascript based web applications.
For full - details see the Jalview 2.7 - release history. -

- Highlights in Jalview Desktop Version 2.7 -

New structure viewer - options: -
- Colour and superimpose 3D structures of complexes and - multi-domain chains using several different alignments
- Drag and drop to associate PDB files with sequences that - have the same name
- Open and superimpose all associated structures for the - current selection
-
New web services for alignment - analysis
Improved graphical user interface for JABAWSservices. -
Sort associated alignment views option in tree viewer
Default colours for shading alignment - by quantitative annotation. -
Jalview Desktop RSS - reader - following important updates at http://www.jalview.org/feeds/desktop/rss -

- -

- Issues Resolved (a select list - see the release history for full details) - -

- Issues in the Jalview Desktop -

Problems viewing associated structures for sequences - retrieved from UNIPROT
Problems viewing Jalview projects from older versions in - version 2.6
Preservation of hidden annotation rows and tree bootstrap - values in projects
Newly added JABAWS servers not always visible in web services - menu

- Issues specific to the JalviewLite Applet -

Layout problems when lots of annotation rows are displayed
<= shown as = in annotation row tooltip
export features raises exception when no features exist
relative URLs not handled properly when used in parameters - and annotation files

- Issues affecting both applet and application -

sequence numbering not preserved in MSF alignment output
sequence associated secondary structure not correctly parsed - in interleaved stockholm
sequences containing lowercase letters are not properly - associated with their pdb files
Jalview PDB file reader does not extract sequence from deoxy - nucleotide chains correctly
Sequence length given in alignment properties window is off - by 1

+ 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.

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. +
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

+ 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.