Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

       Bio::Factory::SequenceStreamI - Interface describing the basics of a Sequence Stream.

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.

FEEDBACK

   Mailing Lists
       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
       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 Bugs
       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://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

       Email jason@bioperl.org

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

   next_seq
        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_seq
        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_factory
        Title   : sequence_factory
        Usage   : $seqio->sequence_factory($seqfactory)
        Function: Get the Bio::Factory::SequenceFactoryI
        Returns : Bio::Factory::SequenceFactoryI
        Args    : none