Skip to content
Snippets Groups Projects
ChangeLog 8.29 KiB
Newer Older
tjc's avatar
tjc committed
Version 12.+
tjc's avatar
tjc committed
	Add support for VCF v3.3 and v4.0.

tjc's avatar
tjc committed
	Add option to show combined coverage plots for multiple BAMs.

tjc's avatar
tjc committed
	Add show_forward_lines and show_reverse_lines as options for switching
	frame lines on and off.
	
tjc's avatar
tjc committed
	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).

tjc's avatar
tjc committed
	Add BamView panel to ACT.

tjc's avatar
tjc committed
	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.
	
tjc's avatar
tjc committed
	Plot multiple coverage plots in BamView when multiple BAM files are
tjc's avatar
tjc committed
	loaded in.

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

tjc's avatar
tjc committed
	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.
tjc's avatar
tjc committed

tjc's avatar
tjc committed
	All graphs can now be configured to be plotted as line graphs
	or heat maps.
	
tjc's avatar
tjc committed
	Added support for BLAST tabular format (-m 8 option) and MSPcrunch 
	format to plot scores.
	
tjc's avatar
tjc committed
	Added support for wiggle (variableStep/fixedStep) plots that can be 
tjc's avatar
tjc committed
	displayed as histograms or heat maps. 
tjc's avatar
tjc committed
	
tjc's avatar
tjc committed
	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.
	
tjc's avatar
tjc committed
    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.
    
tjc's avatar
tjc committed
	Added an option to the Write menu for writing a combination of upstream 
	+ feature + downstream bases for selected features.

tjc's avatar
tjc committed
    Option added in the View->Filter Features menu to search for Duplicate
    Systematic Name Qualifier.

tjc's avatar
tjc committed
    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.

tjc's avatar
tjc committed
    Transfer Annotation Tool (TAT) added to feature editor and Gene
    Builder.

tjc's avatar
tjc committed
	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
tjc's avatar
tjc committed

tjc's avatar
tjc committed
    Use black_belt_mode to suppress warnings when opening Artemis.
tjc's avatar
tjc committed
    
tjc's avatar
tjc committed
    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

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

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

tjc's avatar
tjc committed
    Optimisation of reading in user graphs.

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

tjc's avatar
tjc committed
	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.
tjc's avatar
tjc committed

tjc's avatar
tjc committed
	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.

tjc's avatar
tjc committed
	Provide option to log transform user data plot.
tjc's avatar
tjc committed
	
	Improved error reporting for contig reordering.

tjc's avatar
tjc committed
   	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
	
tjc's avatar
tjc committed
	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.
	
tjc's avatar
tjc committed
	Add -Dread_only option for read only databases.
	
tjc's avatar
tjc committed
	Add option to lazy load feature data from database.
	
Version 10
tjc's avatar
tjc committed

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

tjc's avatar
tjc committed
	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.
tjc's avatar
tjc committed
	
tjc's avatar
tjc committed
	Added "Convert Qualifier of Selected..." option to the Edit menu.
	This allows the user to change the names of qualifiers for all
	selected features.
	
tjc's avatar
tjc committed
	Now using new release of j2ssh (0.2.9). This requires Java1.5+.
tjc's avatar
tjc committed

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

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

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

tjc's avatar
tjc committed
	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.
tjc's avatar
tjc committed
	
	Added -Doffset so that Artemis can be opened at a given base.
tjc's avatar
tjc committed

Version 9

tjc's avatar
tjc committed
	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.

tjc's avatar
tjc committed
	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.

tjc's avatar
tjc committed
	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.
tjc's avatar
tjc committed
	
	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.
tjc's avatar
tjc committed

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

	For Mac users, the option to send search results to the browser will
	display the results in the default browser.
tjc's avatar
tjc committed

	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.