Newer
Older
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
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.
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
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 graphs to be able to adjust their height.
Add redo function to 'Edit' menu. Also enable/disable undo and
redo menu items when available/not available.
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.
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.
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.