What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=7d88e7f5eafbbbd8e2e11aa21b479e5d6c6588d5;hb=d46f2f52b52c1495b92707ab6ad520bb1e465d5e;hp=d66c14cb8728967d5357c37fee3ddeeaeabf0c6a;hpb=14e8b69c8c3c474d77dbdf317565bbf37094185a;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index d66c14c..7d88e7f 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -2,140 +2,55 @@ 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:

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

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!
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. +

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Release	New Features	Issues Resolved
2.06 - 28/9/05	- View annotations in wrapped mode - More options for PCA viewer -	- GUI bugs resolved - Runs with -nodisplay from command line -
2.05b - 15/9/05	- 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 -

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