What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=7d88e7f5eafbbbd8e2e11aa21b479e5d6c6588d5;hb=ef6291f17491f1c426e2cad44021c31f609e2808;hp=965edea3f8725be155776a0a09a739e9704d5d27;hpb=92ae1457a784553ccdb842b122d481ce6c5ff24f;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 965edea..7d88e7f 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,35 +1,56 @@ - -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 ? + +

What's new ?

Jalview Version 2.08

Editing can be locked to the + selection area so that any edits made within the locked area do + not unexpectedly shift other parts 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 features 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 files. +

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

+ +