ChangeLog

Version ??

 	"Set Score Cutoffs" in Artemis popup menu uses existing /scores as
 	the initial min and max values (rather than just 0 and 100).

	Added cache to store the entries retrieved for the object editor.
	
	Implement log4j logging to be displayed in log viewer. Using colour
	coding depending on level of logging.
	
	Added -Doffset so that Artemis can be opened at a given base.

Version 9

	Feature selector can be used to look for features with introns 
	that do no contain the GT/GC start or AG end.

	Contig tool now checks for contigs that contain features that
	span the boundaries of the contigs. These features have to be 
	removed or restricted to the contig boundary before it can 
	carry out contig reordering.

	Fix for converting files from other file formats to
	genbank format.

	Fix rounding problem for long sequences when writting 
	out all bases in FASTA or raw format.

	Cache the start codons (as per stop codon caching),
	to speed their display.

	Combine the extend to next exon and the fix stop codons
  	into one option.

	The feature types that appear on the frame lines can be defined
	by the user via an option ("Frame Line Features...") in the 
	feature display popup menu.
	
	Added to File -> Preferences a user defined selection for display names
	and systematic names. Also extended popup menu option in feature lists 
	to allow the user to be able to select multiple qualifiers to display.

	For entries opened from the remote side of an SSH connection will search
	for results on the remote file system if they are not found locally. They
	are transferred via SSH and then stored locally.

	For Mac users, the option to send search results to the browser will
	display the results in the default browser.

	When automatically generating gene names (under the Edit menu), the user
	can specify the number of zeros to pad the numbering with. e.g if 5 digits are
	selected the format will look like : 00001, 00002 etc.