X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=bd57b81b2859697831859af7babf8ebab04729d5;hb=f850089f8bc67403194f4a1a3b793a46dbb4224a;hp=47819f288c31734c80e49f25d2497c9a848ca9f4;hpb=a9da23fb2862cd01e441858e66684a35675ea3ea;p=jalview.git
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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!
-
-
-
- Release |
- New Features |
- Issues 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 |
- |
- |
-
-
+Jalview Version 2.07
+Sequence Fetcher has been added to quickly
+ retrieve sequences with known ids from several databases.
+Sequence Features enhanced to allow
+ the user to display all features of a Uniprot file on the alignment and subsequently
+ colour, hide or show overlapping features.
+Choose to omit /start-end from sequences when
+ saving files. This is important for saving files to be used by some programs
+ which cannot read the original Jalview sequence output with the appended /start-end.
+PDB structure viewer enhanced. Mapping
+ between sequence and structure has been enhanced, colours on the alignment are
+ reflected in the structure viewer.
+Jalview Applet can read
+ in feature files, PDB files be used as input to HTML form See the website
+ to find out the new parameters available for the Applet Version of Jalview.
+Issues Resolved
+Group Editing is possible with Control and mouse click. Alt key and mouse press
+ does not work as this translates as the middle mouse button, which since 2.04
+ is now used to scroll the alignment and change the font size.
+HTML export now writes groups and features which were previously missing.
+
+See the Release History page for details of all
+ new features and resolved issues.