X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=0382f2225f7b83d424b1b6b660b6eef0c7673e3f;hb=33342a9ee15da4873f9fd94bc2330bc73e7bc51f;hp=090b695a7a3eeb1c22edc4649bca2b00a3a989af;hpb=b84ca14daeb98eae172853154189105c85333257;p=jalview.git
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- Jalview 2.10.2b1 bugfix release
+ What's new in Jalview 2.10.3b1 ?
- This is patch release for 2.10.2. See the release notes for full
- details about the bugs addressed. This release also introduces
- additional improvements to the overview panel, and patches for
- several minor issues including the ability to correctly recover
- cross-references for Uniprot protein sequences from Ensembl.
+ This release - Jalview 2.10.3b1 is the January 2018 patch release for Version 2.10.3 was released in November 2017. The major focus was to
+ improve Jalview's sequence features datamodel and the scalability of
+ the alignment rendering system. The bugs fixed in this release can be found in the 2.10.3b1
+ Release Notes.
-
- What's new in Jalview 2.10.2 ?
-
-
- 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.
+
The highlights for Jalview 2.10.3 include:
- - 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- calculating PCA and different types of tree have been replaced by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.
+ - Faster and more responsive UI when importing and working
+ with wide alignments and handling hundreds and thousands of
+ sequence features
+ - Improved usability with PDB and UniProt Free Text
+ Search dialog, and new tab for retrieval of sequences for lists of
+ IDs.
+
+ - Short names assigned to sequences retrieved from UniProt
+ - Groovy console upgraded to 2.4.12 (improved support for Java 9)
- 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.
+ Remember, please enable the Experimental Features option in
+ the Jalview Desktop's Tools menu, and then restart Jalview
+ if you want to try out features below:
- Annotation transfer between Chimera and Jalview
Two
@@ -139,6 +61,6 @@
the Chimera viewer's Chimera menu allow positional annotation to
be exchanged between Chimera and Jalview.
-
+