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:

         https://github.com/bioperl/bioperl-live/issues

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 inherited 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

   get_Seq_by_version
        Title   : get_Seq_by_version
        Usage   : $seq = $db->get_Seq_by_version('X77802.1');
        Function: Gets a Bio::Seq object by sequence version
        Returns : A Bio::Seq object
        Args    : accession.version (as a string)
        Throws  : "acc.version 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
                  may be 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