Christopher Fields > BioPerl > Bio::Seq::SeqFactory

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Module Version: 1.006924   Source  

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)
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