What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=c260b5a960e861cffb0cc992ca0079664b7f10b0;hb=5ccaaa04373a6f6ae265c43c579adb58421efba0;hp=b40113183b4676c1809f6f1a011ca285c7fbba94;hpb=b25e74cbff1b97e12c1f3b4ea0b1914a13a5c474;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index b401131..3538ff4 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,129 +1,71 @@ - -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
2.05b - 30/8/05	- Choose EPS export as lineart or text - Jar files are executable - Can read in Uracil - maps to unknown residue -	- Known OutOfMemory errors give warning message - Overview window calculated more efficiently - Several GUI bugs 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 ? + + +

+ 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.

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.

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

+ 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 +

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

+ +