NAME¶
Bio::Seq::SeqFactory - Instantiation of generic Bio::PrimarySeqI (or derived)
objects through a factory
SYNOPSIS¶
use Bio::Seq::SeqFactory;
my $factory = Bio::Seq::SeqFactory->new();
my $primaryseq = $factory->create( -seq => 'WYRAVLC',
-id => 'name' );
# Create Bio::Seq instead of Bio::PrimarySeq objects:
my $factory = Bio::Seq::SeqFactory->new( -type => 'Bio::Seq' );
DESCRIPTION¶
This object will build Bio::PrimarySeqI and Bio::SeqI objects generically.
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 _
new¶
Title : new
Usage : my $obj = Bio::Seq::SeqFactory->new();
Function: Builds a new Bio::Seq::SeqFactory object
Returns : Bio::Seq::SeqFactory
Args : -type => string, name of a PrimarySeqI derived class
This is optional. Default=Bio::PrimarySeq.
create¶
Title : create
Usage : my $seq = $seqbuilder->create(-seq => 'CAGT', -id => 'name');
Function: Instantiates new Bio::SeqI (or one of its child classes)
This object allows us to genericize the instantiation of sequence
objects.
Returns : Bio::PrimarySeq object (default)
The return type is configurable using new(-type =>"...").
Args : initialization parameters specific to the type of sequence
object we want. Typically
-seq => $str,
-display_id => $name
type¶
Title : type
Usage : $obj->type($newval)
Function:
Returns : value of type
Args : newvalue (optional)