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.\" ========================================================================
.\"
.IX Title "Bio::Factory::SequenceFactoryI 3pm"
.TH Bio::Factory::SequenceFactoryI 3pm "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Factory::SequenceFactoryI \- This interface allows for generic building of sequences in factories which create sequences (like SeqIO)
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
# do not use this object directly it is an interface
# get a Bio::Factory::SequenceFactoryI object like
.PP
.Vb 2
\&    use Bio::Seq::SeqFactory;
\&    my $seqbuilder = Bio::Seq::SeqFactory\->new(\*(Aq\-type\*(Aq => \*(AqBio::PrimarySeq\*(Aq);
\&
\&    my $seq = $seqbuilder\->create(\-seq => \*(AqACTGAT\*(Aq,
\&                                  \-display_id => \*(Aqexampleseq\*(Aq);
\&
\&    print "seq is a ", ref($seq), "\en";
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
A generic way to build Sequence objects via a pluggable factory.  This
reduces the amount of code that looks like
.PP
.Vb 2
\&  if( $type  eq \*(AqBio::PrimarySeq\*(Aq ) { ... } 
\&  elsif( $type eq \*(AqBio::Seq::RichSeq\*(Aq ) { ... }
.Ve
.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\-at\-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 "create"
.IX Subsection "create"
.Vb 11
\& Title   : create
\& Usage   : my $seq = $seqbuilder\->create(\-seq => \*(AqCAGT\*(Aq, 
\&                                         \-id => \*(Aqname\*(Aq);
\& Function: Instantiates new Bio::PrimarySeqI (or one of its child classes)
\&           This object allows us to genericize the instantiation of sequence
\&           objects.
\& Returns : Bio::PrimarySeqI
\& Args    : initialization parameters specific to the type of sequence
\&           object we want.  Typically 
\&           \-seq        => $str,
\&           \-display_id => $name
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