X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=ed6f5c263624db37d6154d3345604ad82f6b3c89;hb=a4806ceb8d534d99eb00fbf9157ff79c95da0939;hp=04fcc6983b3836269a2dd43571edf3aa744404a3;hpb=11d7be472ca5ea89d69e5bb7882c0058b2c3c4b9;p=jalview.git
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- What's new ?
+ What's new in Jalview 2.10.4b1 ?
-
- Jalview 2.9 has been in development since December 2014. In addition
- to a multitude of bug fixes and minor improvements (both small, and
- rather big!), it also brings major new capabilities for codon-level
- analysis of protein alignments and the retrieval and manipulation of
- structural data.
For the full list of changes, see the
- Jalview 2.9 Release Notes.
-
-
- Highlights in Jalview 2.9
+
This is the first patch release for Jalview 2.10.4. It includes
+ the following new patches:
- - Visualisation, editing and analysis of
- cDNA and Protein alignments
A new Split View window allows linked
- protein and nucleotide sequence alignments to be viewed, edited,
- and analysed as one.
cDNA alignments can also be
- reconstructed from protein alignments calculated by Jalview's web
- services, and update in response to edits in the amino acid view.
To
- start experimenting with cDNA/Protein analysis, jut drop a file
- containing cDNA sequences which code for, and have IDs matching
- proteins in an existing alignment, and Jalview will do the rest.
- - Enhanced Integration of UCSF Chimera
Jalview
- 2.9 provides full support for the use of Chimera to view 3D
- structures linked to alignment views in the Jalview Desktop. We've
- also included support for saving Chimera sessions in Jalview
- project files.
Jalview and Chimera communicate using local
- web server connections, which may cause firewall alerts on some
- systems, but has the advantage of allowing bidirectional
- communication. Communication between Jalview and Chimera is now
- much more responsive, and selected regions in Chimera are now
- shown as highlighted regions in the Jalview desktop.
- - Interactive querying of the PDBe
Jalview
- users can now browse and retrieve 3D structure data from the PDB
- via the PDBe
- Search API (Gutmanas
- et al 2014). Developed in collaboration with the PDBe group at
- EMBL-EBI, the interface allows both structured and free-text
- queries to be performed, and allows automatic selection of the
- most relevant structures for an alignment acording to a variety of
- criteria.
- - Improved support for RNA visualisation
Jalview
- 2.9 integrates the latest version of the VARNA RNA Viewer, and VARNA views
- can also now be stored in Jalview projects. We've also dealt with
- a number of lingering bugs in the VARNA/Jalview interface,
- including the loss of pseudoknots when RNA secondary structure is
- shown VARNA.
- - Protein Secondary Structure predictions
- with JPred4Jalview includes a number of new features for working
- with secondary structure predictions from the JPred4 server. These
- include the ability to automatically hide insertions and highlight
- mutations in an alignment with respect to a reference sequence.
- Jalview 2.9's new scrollable SVG HTML export mode was also
- developed specifically for the JPred4 server.
+ - HGVS nomenclature used for variant annotation retrieved
+ from Uniprot
+ - Uniprot import fails for some sequences (Cannot import
+ features with multiple variant elements)
+ - Clustal files with sequence positions in right-hand column
+ are now parsed correctly
+ - Wrap view - export to SVG - IDs shown but not alignment
+ area in exported graphic
+ - F2/Keyboard mode edits work when Overview window has input
+ focus
+ - Windows specific fixes:
+
+ - Annotation panel set too high when annotation added to
+ view
+ - Updated search paths for Chimera default installation
+ - Windows File Shortcuts can be dragged onto the Jalview
+ Desktop
+ - Drag URL from Chrome, Firefox, IE to Jalview desktop on
+ Windows doesn't open file:
Dragging the currently open
+ URL and links from a page viewed in Firefox or Chrome on
+ Windows is now fully supported.
+ If you are using Edge, only links in the page
+ can be dragged.
+ With Internet Explorer, only the currently open
+ URL in the browser can be dropped onto Jalview.
+
+
+
-
+ Highlights in the 2.10.4 series include:
+
+ - 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.
+