.\" Automatically generated by Pod::Man 4.14 (Pod::Simple 3.40)
.\"
.\" Standard preamble:
.\" ========================================================================
.de Sp \" Vertical space (when we can't use .PP)
.if t .sp .5v
.if n .sp
..
.de Vb \" Begin verbatim text
.ft CW
.nf
.ne \\$1
..
.de Ve \" End verbatim text
.ft R
.fi
..
.\" Set up some character translations and predefined strings.  \*(-- will
.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left
.\" double quote, and \*(R" will give a right double quote.  \*(C+ will
.\" give a nicer C++.  Capital omega is used to do unbreakable dashes and
.\" therefore won't be available.  \*(C` and \*(C' expand to `' in nroff,
.\" nothing in troff, for use with C<>.
.tr \(*W-
.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p'
.ie n \{\
.    ds -- \(*W-
.    ds PI pi
.    if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch
.    if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\"  diablo 12 pitch
.    ds L" ""
.    ds R" ""
.    ds C` ""
.    ds C' ""
'br\}
.el\{\
.    ds -- \|\(em\|
.    ds PI \(*p
.    ds L" ``
.    ds R" ''
.    ds C`
.    ds C'
'br\}
.\"
.\" Escape single quotes in literal strings from groff's Unicode transform.
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.\"
.\" If the F register is >0, we'll generate index entries on stderr for
.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
.\" entries marked with X<> in POD.  Of course, you'll have to process the
.\" output yourself in some meaningful fashion.
.\"
.\" Avoid warning from groff about undefined register 'F'.
.de IX
..
.nr rF 0
.if \n(.g .if rF .nr rF 1
.if (\n(rF:(\n(.g==0)) \{\
.    if \nF \{\
.        de IX
.        tm Index:\\$1\t\\n%\t"\\$2"
..
.        if !\nF==2 \{\
.            nr % 0
.            nr F 2
.        \}
.    \}
.\}
.rr rF
.\" ========================================================================
.\"
.IX Title "Bio::Factory::SequenceStreamI 3pm"
.TH Bio::Factory::SequenceStreamI 3pm "2021-08-15" "perl v5.32.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::Factory::SequenceStreamI \- Interface describing the basics of a Sequence Stream.
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 5
\&  # get a SequenceStreamI object somehow like with SeqIO
\&  use Bio::SeqIO;
\&  my $in = Bio::SeqIO\->new(\-file => \*(Aq< fastafile\*(Aq);
\&  while( my $seq = $in\->next_seq ) {
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This interface is for describing objects which produces
Bio::PrimarySeqI objects or processes Bio::PrimarySeqI objects to a
data stream.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Jason Stajich"
.IX Header "AUTHOR - Jason Stajich"
Email jason@bioperl.org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "next_seq"
.IX Subsection "next_seq"
.Vb 3
\& 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
.Ve
.PP
See Bio::Root::RootI
.SS "write_seq"
.IX Subsection "write_seq"
.Vb 5
\& 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
.Ve
.SS "sequence_factory"
.IX Subsection "sequence_factory"
.Vb 5
\& Title   : sequence_factory
\& Usage   : $seqio\->sequence_factory($seqfactory)
\& Function: Get the Bio::Factory::SequenceFactoryI
\& Returns : Bio::Factory::SequenceFactoryI
\& Args    : none
.Ve