X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=0abd2a7b9501e9f1fffc3bc4456f39ec4af1d50a;hb=06fb1b18865c75aa78186970e74392058444fde4;hp=92ad73f786aca1e2132c406dd7dd7bb91860e130;hpb=a8263b93c9c750a9eefec3098a290c0224bfd7fc;p=jalview.git
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- Jalview 2.10.2b1 bugfix release
+ What's new in Jalview 2.10.4 ?
- This is patch release for 2.10.2. See the release notes.
+ This is the May 2018 release of Jalview, and the last in the 2.10.x series. Jalview 2.10.4 includes:
- - Gaps are now rendered as dark grey in overview window
+ - 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)
- What's new in Jalview 2.10.2 ?
+ The full list of bugs fixed in this release can be found in the 2.10.4
+ Release Notes.
-
- Version 2.10.2 was released in August 2017, and introduced new user
- interface features, improved and more extensible tree and PCA
- analysis, more robust 3D structure viewing with UCSF Chimera and an
- updated service client for JABAWS. The full list of bug fixes and
- new features can be found in the 2.10.2 Release Notes, but
- the highlights are below.
-
-
- - New dialog and faster and more
- configurable Tree and PCA calculations
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- calculating PCA and different types of tree have been replaced by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.
- - Extensible score models
A new
- framework has also been created for the score models used to
- calculate distances between sequences and shade alignments. This
- framework allows import of substitution matrices in NCBI and
- AAIndex format.
PCA Bug Fixes. Jalview's
- implementation of PCA differed in its treatment of gaps and
- non-standard residues. The BLOSUM62 matrix also included a typo
- that affected results. See the 2.10.2 release note
- about score model bugs for details and how to reinstate legacy
- behaviour.
- - 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 JABAWS 2.2 services have been
- updated, so their options and parameters have changed.
- - URL linkouts to other bioinformatics
- databases
New preferences for opening web pages for
- database cross-references via the UK Elixir's EMBL-EBI's MIRIAM
- database and identifiers.org services.
- - 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.
- - Gap count - a.k.a. the Occupancy
- Annotation Row
Another way to filter columns according to
- the presence of gaps is to enable the Occupancy
- Annotation row via Jalview's Preferences. This annotation row
- shows a histogram of the number of aligned residues at each
- column. The Select
- By Annotation dialog now also includes a percentage threshold
- mode, to make it easy to filter alignments to show only those
- columns with a particular fraction of aligned sequences.
- - Recent search history for Find, PDBe and
- Uniprot
Easily repeat a previous search for Find and the free
- text search system (for querying Uniprot and the PDBe).
- - Improved Overview Window
The alignment overview is now easier
- to use when working with alignments of more than 5000 rows and
- columns, and features a new pop-up menu that allows hidden regions
- to be excluded from the overview. It also works with CDS/Protein
- alignments and MSA views in wrapped mode.
- - 3D Structure
Jalview's communication
- with UCSF Chimera has been made more robust, particularly when
- working with many structures and long sequences. Regions in
- structures that correspond to hidden regions in an alignment view
- are now left un-coloured, making it easier to highlight specific
- features in 3D. See below for experimental
- features for exchanging annotation 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.
-
-
- Experimental Features
-
-
- This release of Jalview introduces an Experimental Features
- option in the Jalview Desktop's Tools menu that allows you
- to try out features that are still in development. To access the
- experimental features below - first enable the Tools→Enable
- Experimental Features option, and then restart Jalview.
-
-
-