What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=60769a4cde71ced02fdb6679c244febcb213b7bc;hb=97f7dd4f753e4a95e4d58b2e3818004d353c02c3;hp=b5f5c7876eead6be00bda53d2434f747f09c3d2d;hpb=6fc9aca27f606f6e3a0121597896e1a5dae35c36;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index b5f5c78..60769a4 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,55 +1,99 @@ - -What's new ? - -

What's new ?

Jalview Version 2.08

Editing can be locked to the selection area. - Any edits made within the locked area do not affect the rest of the alignment.

Keyboard editing - press F2 to toggle cursor mode On / Off. For a full list - of keyboard controls, look here.

Create sequence features from searches. - Previously, the regions of sequences highlighted as the result of - searches were added as new regions in the alignment. Now, the sequence region - selected by a search can be used to define named sequences features - attached to the sequence, rather than the alignment. -

Sequence feature display and rendering has also been enhanced, with - the addition of sequence feature groups (which can be used to show - or hide a set of feature types en masse) and user defined - feature colours as well as transparency controls, using the Sequence Feature Settings - window. The Features file - has also been extended to accomodate these enhancements.

Alignment annotation and colouring is also considerably - enhanced. Precalculated symbolic and quantitative annotations (text labels, - secondary structure symbols and multiple scalar graphs) can now be - loaded onto alignments via the Annotation - File. Additionally, the Annotation - Colouring dialog box allows an alignment to be coloured based on - any of the graphed quantities with which it is annotated.

Rendering speed has been improved by disabling anti-aliasing via - the Smooth Fonts - option in the View - menu (its default set in Preferences). In addition, response - times when editing alignments can be reduced by turning off the automatic - calculation of amino acid property Consensus (which has been - reintroduced to the Calculate menu as Autocalculate Consensus).
-

Issues Resolved

Drag & Drop now works on common Linux desktops (at least KDE -and Gnome)
Jalview XML Archive Input/Output is now faster (using an -internal Jalview schema), and sequence description strings are now -preserved in the archive.
Jalview can now correctly read and write MODELLER style -PIR description lines for proteins with a PDB reference. -

See the Release History page for details of all - new features and resolved issues.

- - + + + +What's new ? + + +

+ What's new in Jalview 2.10.2 ? +

+ Full details about Jalview 2.10.2 are in the 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.
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 Find and the free + text search system (for querying Uniprot and the PDBe).

+ 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 + Experimental Features option, and then restart Jalview. +

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.

+ 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. +

+ +