X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=3538ff4b1738f95e0516332b803c139306ed7206;hb=6764c7be2ae71536ef150f5753ab36e585d56e5c;hp=090b695a7a3eeb1c22edc4649bca2b00a3a989af;hpb=b84ca14daeb98eae172853154189105c85333257;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 090b695..3538ff4 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -24,121 +24,48 @@

- Jalview 2.10.2b1 bugfix release -

- 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. -

- 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. + Jalview 2.11 - major and minor new features

Jalview 2.11 introduces support for loading VCF files, and new + filters and shading models for sequence features. Under the hood, + we've addressed many bugs, and also made some important changes in + the way the Jalview desktop is installed and launched.

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Menu entries for - calculating PCA and different types of tree have been replaced by - a single Calculations - dialog box.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.
VCF Support. Proteins and genomic contigs with + chromosomal location annotation (such as protein coding genes + retrieved from Ensembl) can be annotated with variants imported + from a local VCF file.
The Jalview Launcher and Update System
+ Jalview's new installation model means you'll only need to + download and install Jalview once. After installation, Jalview + will automatically keep itself up to date. The launcher also sets + Jalview's memory automatically, so you'll never again have to + manually configure Java's memory settings.
We are grateful to + Install4J who provided us with a free license for their + installation system, and Jalview's over the air update system is + via Getdown.

- 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 + The full list of bugs fixed in this release can be found in the 2.11 Release Notes.

- 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. + Jalview and Java 11, 13, and onwards

Java 11 provides improved performance and better OS + integration, so we now recommend users select our Java 11 Jalview + distribution rather than the legacy Java 8 build.

+ Known Issues - update for 211

Annotation transfer between Chimera and Jalview
Two - new entries in - the Chimera viewer's Chimera menu allow positional annotation to - be exchanged between Chimera and Jalview.
OSX: The 'Open File' dialog for Jalview's Groovy Console + appears with the title 'Save As', and attempting to select a file + to load yields a FileNotFound exception.
The workaround is to first + clear the 'Untitled' filename before selecting the file you wish + to load. +
OSX: Links don't open when clicked on or via the Sequence + or Alignment window popup menu.
OSX (Webstart): JalviewÂ only displays old news feed items