What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=dd536b10e9d2a48ebc4d2f6104455c8d89ea8f55;hb=3e0101470a0b6d41eac74c129f963a6ed0e69e2f;hp=47819f288c31734c80e49f25d2497c9a848ca9f4;hpb=a9da23fb2862cd01e441858e66684a35675ea3ea;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 47819f2..dd536b1 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,115 +1,76 @@ - -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!

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Release	New Features	Issues Resolved
2.05 - 30/8/05	- Edit and annotate in "Wrapped" view -	- Several GUI bugs resolved -
2.04 - 24/8/05	- Hold down mouse wheel & scroll to change font size -	- Improved JPred client reliability - Improved loading of Jalview files -
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 -
2.02 - 18/7/05		- Copy & Paste order of sequences maintains alignment order. -
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. - -
2.0 - 20/6/05	- New codebase -

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

+ What's new ?

+ Jalview 2.8.1 includes new features for group creation, RNA secondary + structure prediction and a host bug fixes. It also includes support + for version 2.1 + of JABA and includes a Spanish translation of its user interface.
+ The highlights are detailed below, and the full list is given in the Jalview 2.8.1 Release Notes. +

The Desktop and web based applet include new keystrokes for + defining and undefining groups, and PAM250 has been added to the range + of score models available for use by the tree and PCA calculations. + The Jalview project file format has also been extended for handling + RNA and protein secondary structure annotation, in anticipation for + new structure based secondary structure support in Jalview 2.8.2.

Internationalisation

Jalview 2.8.1 is the first release to include support for + displaying Jalview's user interface in different languages. In August + 2013, David Roldán-Martinez took on the task of + internationalising Jalview's user interface. He also recruited Sara + Hernández Díaz 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 documented + the process of creating i18n translations to help you get started. +

RNA Secondary Structure Prediction with JABA 2.1

+ This version of Jalview includes a client to access the new services available in JABA v2.1 , which + provides services for RNA consensus secondary structure prediction and + two new alignment programs (GLProbs and MSAProbs).

+ To see how to perform RNA secondary structure predictions like the one below, take a look at the RNAAliFold + client documentation. +

The RNAalifold client was implemented by Jalview's 2013 + summer student, Dan Barton. +

+ +