What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=344c322233d893da5d0fd96edbcb175d510b5380;hb=9d62842028ff8c2f943ddbf82c28f2c31b878620;hp=31b3f1f974e08a6ebe1750ac5af9387a806499f0;hpb=f7fd2fcf425c4a599dbb1440678672eb31cd865a;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 31b3f1f..344c322 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,157 +1,54 @@ - -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
2.07 - 7 /12/05	- PDB Structure Viewer enhanced - Sequence Feature retrieval and display enhanced - Choose to output sequence start-end after sequence name for file output - Sequence Fetcher WSDBFetch@EBI -	- HTML output writes groups and features - Group editing is Control and mouse click - Applet can read feature files, PDB files and can be used for HTML - form input -
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 -

- - + +What's new ? + +

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 +

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.

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