Bio::Factory SequenceStreamI
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Summary
Bio::Factory::SequenceStreamI - Interface describing the basics of a Sequence Stream.
Package variables
No package variables defined.
Inherit
Bio::Root::RootI
Synopsis
  # get a SequenceStreamI object somehow like with SeqIO
use Bio::SeqIO;
my $in = Bio::SeqIO->new(-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
next_seqDescriptionCode
write_seqDescriptionCode
sequence_factoryDescriptionCode
Methods description
next_seqcode    nextTop
 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
write_seqcodeprevnextTop
 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
sequence_factorycodeprevnextTop
 Title   : sequence_factory
Usage : $seqio->sequence_factory($seqfactory)
Function: Get the Bio::Factory::SequenceFactoryI
Returns : Bio::Factory::SequenceFactoryI
Args : none
Methods code
next_seqdescriptionprevnextTop
sub next_seq {
    shift->throw_not_implemented();
}
write_seqdescriptionprevnextTop
sub write_seq {
    shift->throw_not_implemented();
}
sequence_factorydescriptionprevnextTop
sub sequence_factory {
    shift->throw_not_implemented();
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason StajichTop
Email jason@bioperl.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _