Bio
UpdateableSeqI
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Summary
Bio::UpdateableSeqI - Descendant of Bio::SeqI that allows updates
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
See Bio::SeqI for most of the documentation.
See the documentation of the methods for further details.
Description
Bio::UpdateableSeqI is an interface for Sequence objects which are
expected to allow users to perform basic editing functions (update/delete)
on their component SeqFeatures.
Methods
Methods description
Title : delete_feature
Usage : my $orphanlist=$self->delete_feature($feature,$transcript,$gene);
Function: deletes the specified $feature from the given transcript, if $transcript is sent and exists and $feature is a feature of $transcript,
or from $gene if the $feature is a feature of $gene, or from $self if $transcript and $gene are not sent. Keeps track of the features
of the $gene object that may be left as orphans and returns them as a listref.
Example : I want to delete transcript 'abc' of gene 'def', with three exons, leaving only transcript 'ghi' with two exons.
This will leave exons 1 and 3 part of 'ghi', but exon 2 will become an orphan.
my $orphanlist=$seq->delete_feature($transcript{'abc'},undef,$gene{'def'});
$orphanlist is a reference to a list containing $exon{'2'};
Returns : a listref of orphaned features after the deletion of $feature (optional)
Args : $feature - the feature to be deleted
$transcript - the transcript containing the $feature, so that a $feature can be removed from only one transcript when there are multiple
transcripts in a gene.
$gene - the gene containing the $transcript and/or the $feature |
Methods code
sub delete_feature
{ my ($self,$feature,$transcript,$gene) = @_;
$self->throw_not_implemented();
}
1; } | General documentation
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Ewan Birney forced me to this...
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _