Bio::Factory::SequenceFactoryI

NAME

Bio::Factory::SequenceFactoryI - This interface allows for generic building of sequences in factories which create sequences (like SeqIO)

SYNOPSIS

# do not use this object directly it is an interface # get a Bio::Factory::SequenceFactoryI object like

    use Bio::Seq::SeqFactory;
    my $seqbuilder = Bio::Seq::SeqFactory->new('-type' => 'Bio::PrimarySeq');
    my $seq = $seqbuilder->create(-seq => 'ACTGAT',
                                  -display_id => 'exampleseq');
    print "seq is a ", ref($seq), "\n";

DESCRIPTION

A generic way to build Sequence objects via a pluggable factory. This reduces the amount of code that looks like

  if( $type  eq 'Bio::PrimarySeq' ) { ... } 
  elsif( $type eq 'Bio::Seq::RichSeq' ) { ... }

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list: [email protected] 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-at-bioperl.org

APPENDIX

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

create

 Title   : create
 Usage   : my $seq = $seqbuilder->create(-seq => 'CAGT', 
                                         -id => 'name');
 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