What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=0abd2a7b9501e9f1fffc3bc4456f39ec4af1d50a;hb=dcda5b75e1bbbce40799573d39d6e7298a17b361;hp=88e8ee9114fe5b7fe723e4d17d314de97798dbfa;hpb=c78133920a45e1b5b0b1bea5807f3ae880425914;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 88e8ee9..0abd2a7 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,103 +1,50 @@ + * 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 2.10.4 ? +

+ This is the May 2018 release of Jalview, and the last in the 2.10.x series. Jalview 2.10.4 includes: +

Numerous efficiency improvements in the renderer and overview when working with large alignments with lots of hidden columns
Use of HTTPS when connecting to Uniprot, Ensembl and other EBI web services
Critical patches for running Jalview on OSX with Java 10
Easier adjustment of the Alignment ID panel and Annotation panel
Improved support for mapping between 3D Structures and Uniprot Protein Sequences
Improved support for discovering CDS and transcripts for Proteins and Ensembl gene IDs
New buttons on the Structure Chooser for adding structures + to an existing view, and disabling automatic superposition + according to linked alignments
Annotation transfer between Chimera and Jalview (formerly only + available in 'Experimental' mode)

+ The full list of bugs fixed in this release can be found in the 2.10.4 + Release Notes. +