What's new ?
++ What's new in Jalview 2.10.1 ? +
++ Jalview 2.10.1 was released on 29th November 2016. Full details are + in the Jalview 2.10.1 + Release Notes, but the highlights are below. This is also the + first release to include contributions from Kira Mourão, who + joined Jalview's core development team in October 2016. +
+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.
+
+ Warning dialog about updating
+ your configured URL links
In the desktop prior to Jalview
+ 2.10.1, the only way to configure custom links for a particular
+ database cross-reference for a sequence was to give it a name that exactly
+ matched the database source, and a regular expression for filtering
+ out any spurious matches generated when the custom linked was tested
+ against the Sequence's ID string. Since the introduction of the
+ $DB_ACCESSION$ token, however, $SEQUENCE_ID$ will not be used for
+ database cross-reference accession strings, and if you have custom
+ links configured, Jalview will raise a warning message so let you
+ know that you may need to update your links to use $DB_ACCESSION$.
+