What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2FwhatsNew.html;h=79cf7c98197d9c18e8884964fbeb4c5d7f93cc17;hb=936d30a2eea9e94c2bb221025e58d7e9ed747262;hp=b35c9ae0588bc3566ffbe465d14050ba8f87eb2b;hpb=24974fd5af8b5c2f223cc8f8c0f2f4beb8c4d509;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index b35c9ae..79cf7c9 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,94 +1,72 @@ - -What's new ? - -

What's new ?

If you are reading this then you will already have seen some of the recent changes - made to Jalview.
- Jalview takes advantage of some of the more recent user interface developments - in the Java programming language. For instance Jalview is now a multi windowed - application, this keeps all your Jalview windows neatly together in one main - application window.

If you were familiar with the original Jalview, here is a list of important - features you should know about the current development:

Editing sequences is no longer the default when mouse clicking the alignment. - Instead, mouse clicking on the alignment creates a "selection region" - which may be full sequences or groups of residues.
To insert or edit the gaps in one sequence in alignment, the "Shift" - key must be held down when dragging the mouse.
To insert or edit gaps for a group of sequences, the "Alt" key - (or in X windows the "Control" key) must be held down.
Selecting colour schemes in the colour menu either sets just the "background" - colourscheme for the alignment, or - when the tickbox "Apply colour to - all groups" is ticked, applies the scheme to the background and all groups - defined on the alignment.
Use the right mouse button (apple and click on the Mac) whilst the pointer - is within the selection area to access the "define" region menu - to define a new region, give it a name, and change its colourscheme and display - properties.
Conservation is automatically updated whenever the alignment is edited
There is no "quick draw" option
Edits can be undone, and redone!

- - - - - - - - - - - - - - - - - - - - - - - - - - -

Release	New Features	Issues Resolved
2.0 - 20/6/05	- New codebase -
2.01 - 12/7/05	- Use delete key for deleting selection. - Use Mouse wheel to scroll sequences. - Help file updated to describe how to add alignment annotations. - Version and build date written to build properties file. - InstallAnywhere installation will check for updates at launch of Jalview. -	- Delete gaps bug fixed. - FileChooser sorts columns. - Can remove groups one by one. - Filechooser icons installed. - Finder ignores return character when searching. Return key will initiate - a search. - -
2.02 - 18/7/05		- Copy & Paste order of sequences maintains alignment order. -
2.03 - 18/8/05	- Set Proxy server name and port in preferences - Multiple URL links from sequence ids - User Defined Colours can have a scheme name and added to Colour Menu - Choose to ignore gaps in consensus calculation - Unix users can set default web browser - Runs without GUI for batch processing - Dynamically generated Web Service Menus -	- InstallAnywhere download for Sparc Solaris -

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

+ What's new ?
Jalview 2.8.0b1 is a bugfix + release for Jalview version 2.8.
As usual you can find the + highlights below, and the comprehensive list is given in the Jalview 2.8.0b1 Release Notes. +

+ This bug fix release includes numerous minor enhancements made over + the last 12 months. Importantly, it is also the first release that + provides Jalview as a trusted application, signed with a certificate + donated to us by Certum. +

+ Enhancements and new features +

Allow disorder predictions to be made on the current + selection (or visible selection) in the same way that JPred works
allow import of data from gzipped files
Improved per-sequence 'colour-by-annotation' performance
Support '' style escaping of quotes in Newick files
group options for JABAWS service by command line name
Select primary source when selecting authority in database + fetcher GUI
COMBINE statement uses current SEQUENCE_REF and GROUP_REF + scope to group annotation rows
add .mfa to FASTA file extensions recognised by Jalview
groovy scripting for headless jalview operation
Output in Stockholm format

+ Bug fixes +

Uniprot and PDB database cross-reference fetching works + properly
'View all structures' in the desktop is more reliable
Web services parameter dialog box shows the options enabled + for different presets
Interactive creation of RNA secondary structure works more + smoothly
Keyboard mode 'P' command jumps to the right place
Improved support for parsing database cross-references via + Stockholm and Rfam database
Improved semantics in annotation files for grouping + annotation rows associated with particular sequences and groups
More robust DNA->Amino acid translation
Improved Headless-mode operation for DAS annotation + retrieval, groovy script execution and alignment figure generation
annotation label tooltip text needs to be wrapped

+ +