Bio::Factory
SequenceStreamI
Summary
Bio::Factory::SequenceStreamI - Interface describing the basics of a Sequence Stream.
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
# get a SequenceStreamI object somehow like with SeqIO
use Bio::SeqIO;
my $in = new Bio::SeqIO(-file => '< fastafile');
while( my $seq = $in->next_seq ) {
}
Description
This interface is for describing objects which produces
Bio::PrimarySeqI objects or processes Bio::PrimarySeqI objects to a
data stream.
Methods
Methods description
Title : next_seq
Usage : $seq = stream->next_seq
Function: Reads the next sequence object from the stream and returns it.
Certain driver modules may encounter entries in the stream that
are either misformatted or that use syntax not yet understood
by the driver. If such an incident is recoverable, e.g., by
dismissing a feature of a feature table or some other non-mandatory
part of an entry, the driver will issue a warning. In the case
of a non-recoverable situation an exception will be thrown.
Do not assume that you can resume parsing the same stream after
catching the exception. Note that you can always turn recoverable
errors into exceptions by calling $stream->verbose(2).
Returns : a Bio::Seq sequence object
Args : none
See Bio::Root::RootI |
Title : write_seq
Usage : $stream->write_seq($seq)
Function: writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args : Bio::Seq object |
Title : sequence_factory
Usage : $seqio->sequence_factory($seqfactory)
Function: Get the Bio::Factory::SequenceFactoryI
Returns : Bio::Factory::SequenceFactoryI
Args : none |
Methods code
sub next_seq
{ shift->throw_not_implemented(); } | sub write_seq
{ shift->throw_not_implemented(); } | sub sequence_factory
{ shift->throw_not_implemented(); } | General documentation
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| AUTHOR - Jason Stajich | Top |
Additional contributors names and emails here
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _