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README

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  • ChangeLog 8.09 KiB
    Version 12.+
    	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.