ChangeLog

Version XX
	Shortcut changes made in the 'Preferences' menu are saved between sessions (the 
	shortcut_cache flag in the options file can be used to turn this on/off).
	
	More support for GTF format to show CDS and exons as joined features.

	BAM record list option added to display as a list the reads and their
	properties.
	
	Add options for loading graph, BAM and VCF files into ACT from the 
	command line. Numbers are used to associate the file with a particular
	sequence. e.g. add a BAM to the first (top) sequence in ACT:
	act -Dbam1=/pathToFile/file.bam 
	or, to add a userplot to the second sequence:
	act -Duserplot2=/pathToFile/userPlot

Version 13.2.0
	Added option to provide overview of the variation sites.

	Change BamView filter to enable filtering in and out based on
	reads flag.
	
	Add read count and RPKM calculations to BamView.

	Add option in BamView to clone the alignment panel.
	
	Create features option for VCF records.
	
	Unit tests added for writing VCF/BCF sequences.

	Add new Coverage view to BamView. It automatically switches to this view
	on zooming out.

	Add options to write out or view FASTA sequences from VCF/BVF variation
	data.

Version 13
	Add support for reading in indexed BCF (Binary VCF) files.
	
	Memory optimisation of codon caching, reducing the memory footprint.
	
	It is now possible to add BAM, VCF and BCF files from the command line using the 
	JVM bam option, e.g. art -Dbam=/pathToFile/file.bam 
	and for multiple BAM's/VCF's this is comma separated
	art -Dbam='/pathToFile/file1.bam,/pathToFile/file2.bam', it
	can also read the BAM's from URL's.
	
	Added option to display orientation of reads in BamView.

	In Bamview, display reads that are split over introns so that the exon boundaries can 
	be identified by colouring the line between the aligned blocks grey.
	
	Add VCF panel to ACT.
	
	Support added to read indexed fasta sequence files. An index file is created
	using SAMtools.

	Add support for VCF v3.3 and v4.0.

	Add option to show combined coverage plots for multiple BAMs.

	Add show_forward_lines and show_reverse_lines as options for switching
	frame lines on and off.
	
	Add an option to delete qualifiers in the Find/Replace tool.

	Artemis can read in a set of zipped search results (e.g. blastp/blastp.zip).

	Add BamView panel to ACT.

	Fix for writing EMBL files out from GFF entries.

	An option has been added in BamView to colour reads by the colour 
	used in the coverage plot - useful when looking at multiple BAM files.
	
	Plot multiple coverage plots in BamView when multiple BAM files are
	loaded in.

Version 12
	It is now possible to add user plots from the command line using the 
	JVM userplot option, e.g. art -Duserplot=/pathToFile/userPlot 
	and for multiple plots this is comma separated
	art -Duserplot='/pathToFile/userPlot1,/pathToFile/userPlot2', it
	can also read the plots from URL's.

	Added support to be able to read BAM files to display read alignments.
	It uses picard (http://picard.sourceforge.net/) to read from the BAM file
	and so requires Artemis to be run with Java 1.6.

	All graphs can now be configured to be plotted as line graphs
	or heat maps.
	
	Added support for BLAST tabular format (-m 8 option) and MSPcrunch 
	format to plot scores.
	
	Added support for wiggle (variableStep/fixedStep) plots that can be 
	displayed as histograms or heat maps. 
	
	Added a new user plot file format with the first column specifying
	a base position.
	
	More configure options have been added to the graphs to enable
	configuration of the graph line style and size.
	
	GoTo directory option added to file manager to assist navigation.
	
    The database manager is cached between sessions (this can is on by default 
    and can be switched off with -Ddatabase_manager_cache_off). There is an 
    option under the File menu to clear this cache.
    
    A checkbox has been added to the window for adding ortholog/paralog links
    in the Gene Builder. If this is selected it adds links between existing 
    ortholog/paralogs and the new ortholog/paralog. By default this is off.
    
    An option has been added to the database manager to display polypeptide 
    domains in the feature display (as well as the protein map in the Gene
    Builder).
    
    An option has been added to the Run menu for doing a search of the Pfam
    database.
    
	Added an option to the Write menu for writing a combination of upstream 
	+ feature + downstream bases for selected features.

    Option added in the View->Filter Features menu to search for Duplicate
    Systematic Name Qualifier.

    LookSeq analysis panel can be displayed by setting the lookseq 
    value in the options file. An option under the Display menu then
    is used to shows the LookSeq read alignment panel in Artemis.

    Added options to set the minimum and maximum values of the plots.

    Transfer Annotation Tool (TAT) added to feature editor and Gene
    Builder.

	New graph popup menu option to show the values and average for
	a selected range.
	
	Added product_cv database option to define if the product is
	stored as a controlled vocabulary or as a feature property (featureprop).

Version 11

    Use black_belt_mode to suppress warnings when opening Artemis.
    
    Script (writedb_entry) added to make it easier to write out 
    multiple entries as EMBL / GFF files from chado. This uses Artemis 
    read-write libraries and does not require each sequence to be 
    launched from the database. For command line help run: 
    etc/writedb_entry -help

	On MacOSX - enable dropping files on Artemis application to open sequences
	with file extensions: gff, embl, EMBL, genbank, gbk, fasta, seq, art and 
	dna (defined in Artemis.app/Contents/Info.plist).

	Add NCBI search link to run menu. This transfers the sequence automatically
	to the NCBI web page.
	
	Add support for writing Sequin table format.
	
	Added print to PostScript option in Artemis and ACT.

    Optimisation of reading in user graphs.

	New Edit->Selected Feature(s)->Convert Keys option to convert
	keys of selected features.

	New Edit menu option for finding and replacing qualifier text. This
	has an option for boolean searches (e.g. and, or, &, |) of qualifier
	text. This includes an option to search for duplicate qualifiers.

	Implemented a commit manager for the database mode. This
	highlights transactions that produce an error.
	
	Make the chado transaction log messages more human readable.

    Add ability to write file formats from Artemis in database mode.
    With option to collapse the gene hierarchy (gene, transcript, exon) 
    into a CDS feature.

	Graphs are now added to a split pane. So that their size can be 
	defined by dragging the divider at the bottom of the graphs.

	Provide option to log transform user data plot.
	
	Improved error reporting for contig reordering.

   	Fix for creating intergenic features for overlapping CDS's. Also
   	add note based on which one of the 4 cases with respect to the 
   	flanking CDS it belongs to, i.e.:
 	IGR-F (forward):  cds> IGR cds>
	IGR-R (reverse): <cds IGR <cds
	IGR-B (both): <cds IGR cds>
	IGR-X: cds> IGR <cds
	
	Add option to preferences for defining contig ordering features.

	Added option to "Create features from graph peaks". For a graph 
	this creates features in regions above a given cut-off and above 
	a given feature size.
	
	Add -Dread_only option for read only databases.
	
	Add option to lazy load feature data from database.
	
Version 10

	Add redo function to 'Edit' menu. Also enable/disable undo and
	redo menu items when available/not available.
	
	Add option to replace selected bases in 'Edit' menu.
	
	Option to create features in intergenic regions added.

	Feature editor now marks hyperlinks to SWALL, EMBL, UniProt, 
	PMID, PubMed, InterPro, OrthoMCLDB, Pfam that are opened in 
	the browser. Now configured in the options file.
	
	Added "Convert Qualifier of Selected..." option to the Edit menu.
	This allows the user to change the names of qualifiers for all
	selected features.
	
	Now using new release of j2ssh (0.2.9). This requires Java1.5+.

	Implemented option for ORF creation to take into account boundaries
	of multiple fasta sequences, so that they do not cross them.

	Implemented the ability to run and store fasta and blast search 
	results for multiple databases... E.g. fasta searches on uniprot 
	and on user's own database, stored in multiple fasta_file qualifiers.

 	"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.