X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=169e7fec8754f000648e89b9b468679783aa82dd;hb=a990c2c6facfd04d61d316dcafba31d03747d162;hp=a016a3514c48a7c2bd43d6f5df8e86690504f265;hpb=3c9a109fe89504b4713bfaf612275edc8c07e433;p=jalview.git
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index a016a35..169e7fe 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -1,52 +1,143 @@
+ -->
What's new ?
-
- What's new ?
Jalview 2.8.1 includes a range of new features developed in the last 12 months.
As usual you can find the
- highlights below, and the comprehensive list is given in the Jalview 2.8.1 Release Notes.
-
- Internationalisation
-
- In August 2013, David Róldan-Martinez took on the task of
- internationalising Jalview's user interface. He also recruited Sara
- Hernández DÃaz and Laura Ferrandis Martinez who created Jalview's
- first spanish user interface translation.
If you notice any
- problems, or would like to help translate Jalview's user interface
- into other languages, head over to issues.jalview.org
- and put in a feature request describing the translations you can
- provide to the i18n
- component.
- David has also put together some documentation about getting started with i18n translations
-
- Enhancements and new features
-
- Bug fixes
-
+
+ Jalview 2.10.2b1 bugfix release
+
+
+ This is patch release for 2.10.2. See the release notes.
+
+
+ - Gaps are now rendered as dark grey in overview window
+
+
+ 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.
+
+
+ - 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+ calculating PCA and different types of tree have been replaced by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.
+
+
+