What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2FwhatsNew.html;h=651292e0b5fa6c4ba15bda5a770cab93160a03b1;hb=cbc6aa4a407ef66ae0f5b54fd8dbcd6018a2515a;hp=965edea3f8725be155776a0a09a739e9704d5d27;hpb=92ae1457a784553ccdb842b122d481ce6c5ff24f;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 965edea..651292e 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,35 +1,50 @@ -What's new ? + +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!

What's new ?

+ +

Jalview Version 2.2

Multiple views with different styles, colours, hidden regions for +one alignment

Easily add, amend and delete sequence features

"Reload" alignment from File or URL to revert to +original

"Save" to current filename or "Save As" to +new filename

New "New Window" button on the +"Output To Textbox" opens output window for quick 'sequence +editing'.

Set different text colour for dark or light background

Right align sequence ids

Set colour of lower case residues in a user defined colour scheme +

Menu Rearrangements: New Format for alignment +layout and Select for region selection.

Menu item accelerator keys added

Control-V pastes sequences to active window, Control-Shift-V +pastes to a new window.

Raise/Minimise alignment and all associated windows from desktop +window's window menu

Select and colour whole branches of a tree

'New Window' button on the 'Output to Text box' alignment output +option to open a new alignment window after editing.

Issues Resolved

Optimisations for large alignments: faster multithreaded +calculations and Undo/Redo system.

Remove empty columns - if empty columns exist at the end of the +alignment bug fixed.

DAS feature fetching slowed down, doesn't overload DAS servers

DAS feature fetching can be cancelled

Correct display of > and < symbols for feature descriptions +without explicit <html> tags.

Zoom working in PCA viewer

Sequence Descriptions retained after running a web service

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