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Bio::DB::SeqI(3)      User Contributed Perl Documentation     Bio::DB::SeqI(3)

NAME
       Bio::DB::SeqI - Abstract Interface for Sequence databases

SYNOPSIS
	  # get a Bio::DB::SeqI somehow

	  $seq = $seqdb->get_Seq_by_id('some-id');
	  $seq = $seqdb->get_Seq_by_acc('some-accession-number');

	  @ids = $seqdb->get_all_ids();
	  $stream = $seqdb->get_PrimarySeq_stream();
	  while((my $seq = $stream->next_seq()) {
	     # $seq is a PrimarySeqI compliant object
	  }

DESCRIPTION
       Abstract interface for a sequence database

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 one
       of 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:

	 http://bugzilla.open-bio.org/

AUTHOR - Ewan Birney
       Email birney@ebi.ac.uk

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

Methods inherieted from Bio::DB::RandomAccessI
   get_Seq_by_id
	Title	: get_Seq_by_id
	Usage	: $seq = $db->get_Seq_by_id('ROA1_HUMAN')
	Function: Gets a Bio::Seq object by its name
	Returns : a Bio::Seq object
	Args	: the id (as a string) of a sequence
	Throws	: "id does not exist" exception

   get_Seq_by_acc
	Title	: get_Seq_by_acc
	Usage	: $seq = $db->get_Seq_by_acc('X77802');
	Function: Gets a Bio::Seq object by accession number
	Returns : A Bio::Seq object
	Args	: accession number (as a string)
	Throws	: "acc does not exist" exception

Methods [that were] specific for Bio::DB::SeqI
   get_PrimarySeq_stream
	Title	: get_PrimarySeq_stream
	Usage	: $stream = get_PrimarySeq_stream
	Function: Makes a Bio::SeqIO compliant object
		  which provides a single method, next_seq
	Returns : Bio::SeqIO
	Args	: none

   get_all_primary_ids
	Title	: get_all_ids
	Usage	: @ids = $seqdb->get_all_primary_ids()
	Function: gives an array of all the primary_ids of the
		  sequence objects in the database. These
		  maybe ids (display style) or accession numbers
		  or something else completely different - they
		  *are not* meaningful outside of this database
		  implementation.
	Example :
	Returns : an array of strings
	Args	: none

   get_Seq_by_primary_id
	Title	: get_Seq_by_primary_id
	Usage	: $seq = $db->get_Seq_by_primary_id($primary_id_string);
	Function: Gets a Bio::Seq object by the primary id. The primary
		  id in these cases has to come from $db->get_all_primary_ids.
		  There is no other way to get (or guess) the primary_ids
		  in a database.

		  The other possibility is to get Bio::PrimarySeqI objects
		  via the get_PrimarySeq_stream and the primary_id field
		  on these objects are specified as the ids to use here.
	Returns : A Bio::Seq object
	Args	: accession number (as a string)
	Throws	: "acc does not exist" exception

perl v5.14.1			  2011-07-22		      Bio::DB::SeqI(3)
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