X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;fp=help%2Fhtml%2FwhatsNew.html;h=2b792e0fcf98496c5a0e8b76bd305788221b3830;hb=1ce5693613d1fa2747d55e1eb3231c742120d4a5;hp=60769a4cde71ced02fdb6679c244febcb213b7bc;hpb=d5d8a0a8658cbd90b265210d2d6c96b64c889d60;p=jalview.git
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@@ -26,56 +26,86 @@
What's new in Jalview 2.10.2 ?
-
- Full details about Jalview 2.10.2 are in the Release Notes, but the
+
This August 2018 release of Jalview introduces 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 UI, and faster and more configurable
- implementation for PCA, Neighbour-Joining and UPGMA Trees
- 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- been replaced by a single Calculations dialog box.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. A new framework has
- also been created for the score models used to calculate distances
- between sequences. This framework allows import of substitution
- matrices in NCBI and AAIndex format, and custom score models to be
- created via a groovy script.
+ - 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+ calculating PCA and different types of tree have been replaced by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 services have been updated, so
- their options and parameters have changed.
- - 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.
-
- - Recent search histories for
+
- 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.
+ - 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 includes a new option in the Jalview Desktop
- that allows you to try out features that are still in development.
- To access the features described below, please first enable the Tools→Enable
+ 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.
@@ -84,16 +114,6 @@
the Chimera viewer's Chimera menu allow positional annotation to
be exchanged 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.
-
+