bio::factory::sequencefactoryi(3pm) [debian man page]

Bio::Factory::SequenceFactoryI(3pm)			User Contributed Perl Documentation		       Bio::Factory::SequenceFactoryI(3pm)

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), "
";

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.

	 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://redmine.open-bio.org/projects/bioperl/

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

perl v5.14.2							    2012-03-02				       Bio::Factory::SequenceFactoryI(3pm)

Bio::Assembly::Singlet(3pm)				User Contributed Perl Documentation			       Bio::Assembly::Singlet(3pm)

NAME

       Bio::Assembly::Singlet - Perl module to hold and manipulate
			    singlets from sequence assembly contigs.

SYNOPSIS

	   # Module loading
	   use Bio::Assembly::IO;

	   # Assembly loading methods
	   $aio = Bio::Assembly::IO->new( -file   => 'test.ace.1',
					  -format => 'phrap'	  );

	   $assembly = $aio->next_assembly;
	   foreach $singlet ($assembly->all_singlets) {
	     # do something
	   }

	   # OR, if you want to build the singlet yourself,

	   use Bio::Assembly::Singlet;
	   $singlet = Bio::Assembly::Singlet->new(
	       -id     => 'Singlet1',
	       -seqref => $seq
	   );

DESCRIPTION

       A singlet is a sequence that phrap was unable to align to any other sequences.

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 lists  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 the bugs and their resolution.  Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Chad S. Matsalla
       bioinformatics1 at dieselwurks.com

APPENDIX

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

   new
	   Title   : new
	   Usage   : $singlet = $io->new( -seqref => $seq )
	   Function: Create a new singlet object
	   Returns : A Bio::Assembly::Singlet object
	   Args    : -seqref => Bio::Seq-compliant sequence object for the singlet

   seqref
	   Title   : seqref
	   Usage   : $seqref = $singlet->seqref($seq);
	   Function: Get/set the sequence to which this singlet refers
	   Returns : A Bio::Seq-compliant object
	   Args    : A Bio::Seq-compliant or Bio::Seq::Quality object

   _seq_to_singlet
	   Title   : _seq_to_singlet
	   Usage   : $singlet->seqref($seq)
	   Function: Transform a sequence into a singlet
	   Returns : 1 for sucess
	   Args    : A Bio::Seq-compliant object

perl v5.14.2							    2012-03-02					       Bio::Assembly::Singlet(3pm)