Provided by: libbio-perl-perl_1.6.901-2_all bug


       Bio::PrimarySeqI - Interface definition for a Bio::PrimarySeq


           # Bio::PrimarySeqI is the interface class for sequences.
           # If you are a newcomer to bioperl, you might want to start with
           # Bio::Seq documentation.

           # Test if this is a seq object
           $obj->isa("Bio::PrimarySeqI") ||
             $obj->throw("$obj does not implement the Bio::PrimarySeqI interface");

           # Accessors
           $string    = $obj->seq();
           $substring = $obj->subseq(12,50);
           $display   = $obj->display_id();       # for human display
           $id        = $obj->primary_id();       # unique id for this object,
                                                  # implementation defined
           $unique_key= $obj->accession_number(); # unique biological id

           # Object manipulation
           eval {
                  $rev = $obj->revcom();
           if( $@ ) {
                  $obj->throw("Could not reverse complement. ".
                           "Probably not DNA. Actual exception\n$@\n");

           $trunc = $obj->trunc(12,50);
           # $rev and $trunc are Bio::PrimarySeqI compliant objects


       This object defines an abstract interface to basic sequence information - for most users
       of the package the documentation (and methods) in this class are not useful - this is a
       developers-only class which defines what methods have to be implmented by other Perl
       objects to comply to the Bio::PrimarySeqI interface. Go "perldoc Bio::Seq" or "man
       Bio::Seq" for more information on the main class for sequences.

       PrimarySeq is an object just for the sequence and its name(s), nothing more. Seq is the
       larger object complete with features. There is a pure perl implementation of this in
       Bio::PrimarySeq. If you just want to use Bio::PrimarySeq objects, then please read that
       module first. This module defines the interface, and is of more interest to people who
       want to wrap their own Perl Objects/RDBs/FileSystems etc in way that they "are" bioperl
       sequence objects, even though it is not using Perl to store the sequence etc.

       This interface defines what bioperl considers necessary to "be" a sequence, without
       providing an implementation of this, an implementation is provided in Bio::PrimarySeq. If
       you want to provide a Bio::PrimarySeq-compliant object which in fact wraps another
       object/database/out-of-perl experience, then this is the correct thing to wrap, generally
       by providing a wrapper class which would inherit from your object and this
       Bio::PrimarySeqI interface. The wrapper class then would have methods lists in the
       "Implementation Specific Functions" which would provide these methods for your object.


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AUTHOR - Ewan Birney



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

Implementation Specific Functions

       These functions are the ones that a specific implementation must define.

        Title   : seq
        Usage   : $string = $obj->seq()
        Function: Returns the sequence as a string of letters. The
                  case of the letters is left up to the implementer.
                  Suggested cases are upper case for proteins and lower case for
                  DNA sequence (IUPAC standard), but implementations are suggested to
                  keep an open mind about case (some users... want mixed case!)
        Returns : A scalar
        Status  : Virtual

        Title   : subseq
        Usage   : $substring = $obj->subseq(10,40);
        Function: Returns the subseq from start to end, where the first base
                  is 1 and the number is inclusive, i.e. 1-2 are the first two
                  bases of the sequence.

                  Start cannot be larger than end but can be equal.

        Returns : A string
        Args    :
        Status  : Virtual

        Title   : display_id
        Usage   : $id_string = $obj->display_id();
        Function: Returns the display id, also known as the common name of the Sequence

                  The semantics of this is that it is the most likely string
                  to be used as an identifier of the sequence, and likely to
                  have "human" readability.  The id is equivalent to the ID
                  field of the GenBank/EMBL databanks and the id field of the
                  Swissprot/sptrembl database. In fasta format, the >(\S+) is
                  presumed to be the id, though some people overload the id
                  to embed other information. Bioperl does not use any
                  embedded information in the ID field, and people are
                  encouraged to use other mechanisms (accession field for
                  example, or extending the sequence object) to solve this.

                  Notice that $seq->id() maps to this function, mainly for
                  legacy/convenience reasons.
        Returns : A string
        Args    : None
        Status  : Virtual

        Title   : accession_number
        Usage   : $unique_biological_key = $obj->accession_number;
        Function: Returns the unique biological id for a sequence, commonly
                  called the accession_number. For sequences from established
                  databases, the implementors should try to use the correct
                  accession number. Notice that primary_id() provides the
                  unique id for the implemetation, allowing multiple objects
                  to have the same accession number in a particular implementation.

                  For sequences with no accession number, this method should return
        Returns : A string
        Args    : None
        Status  : Virtual

        Title   : primary_id
        Usage   : $unique_implementation_key = $obj->primary_id;
        Function: Returns the unique id for this object in this
                  implementation. This allows implementations to manage their
                  own object ids in a way the implementaiton can control
                  clients can expect one id to map to one object.

                  For sequences with no accession number, this method should
                  return a stringified memory location.

        Returns : A string
        Args    : None
        Status  : Virtual

        Title   : can_call_new
        Usage   : if( $obj->can_call_new ) {
                    $newobj = $obj->new( %param );
        Function: Can_call_new returns 1 or 0 depending
                  on whether an implementation allows new
                  constructor to be called. If a new constructor
                  is allowed, then it should take the followed hashed
                  constructor list.

                  $myobject->new( -seq => $sequence_as_string,
                                  -display_id  => $id
                                  -accession_number => $accession
                                  -alphabet => 'dna',
        Returns : 1 or 0
        Args    :

        Title   : alphabet
        Usage   : if( $obj->alphabet eq 'dna' ) { /Do Something/ }
        Function: Returns the type of sequence being one of
                  'dna', 'rna' or 'protein'. This is case sensitive.

                  This is not called "type" because this would cause
                  upgrade problems from the 0.5 and earlier Seq objects.

        Returns : A string either 'dna','rna','protein'. NB - the object must
                  make a call of the alphabet, if there is no alphabet specified it
                  has to guess.
        Args    : None
        Status  : Virtual

        Title   : moltype
        Usage   : Deprecated. Use alphabet() instead.

Optional Implementation Functions

       The following functions rely on the above functions. An implementing class does not need
       to provide these functions, as they will be provided by this class, but is free to
       override these functions.

       The revcom(), trunc(), and translate() methods create new sequence objects. They will call
       new() on the class of the sequence object instance passed as argument, unless
       can_call_new() returns FALSE. In the latter case a Bio::PrimarySeq object will be created.
       Implementors which really want to control how objects are created (eg, for object
       persistence over a database, or objects in a CORBA framework), they are encouraged to
       override these methods

        Title   : revcom
        Usage   : $rev = $seq->revcom()
        Function: Produces a new Bio::PrimarySeqI implementing object which
                  is the reversed complement of the sequence. For protein
                  sequences this throws an exception of "Sequence is a
                  protein. Cannot revcom".

                  The id is the same id as the original sequence, and the
                  accession number is also indentical. If someone wants to
                  track that this sequence has be reversed, it needs to
                  define its own extensionsj.

                  To do an inplace edit of an object you can go:

                  $seq = $seq->revcom();

                  This of course, causes Perl to handle the garbage
                  collection of the old object, but it is roughly speaking as
                  efficient as an inplace edit.

        Returns : A new (fresh) Bio::PrimarySeqI object
        Args    : None

        Title   : trunc
        Usage   : $subseq = $myseq->trunc(10,100);
        Function: Provides a truncation of a sequence.
        Returns : A fresh Bio::PrimarySeqI implementing object.
        Args    : Two integers denoting first and last base of the sub-sequence.

        Title   : translate
        Usage   : $protein_seq_obj = $dna_seq_obj->translate

                  Or if you expect a complete coding sequence (CDS) translation,
                  with initiator at the beginning and terminator at the end:

                  $protein_seq_obj = $cds_seq_obj->translate(-complete => 1);

                  Or if you want translate() to find the first initiation
                  codon and return the corresponding protein:

                  $protein_seq_obj = $cds_seq_obj->translate(-orf => 1);

        Function: Provides the translation of the DNA sequence using full
                  IUPAC ambiguities in DNA/RNA and amino acid codes.

                  The complete CDS translation is identical to EMBL/TREMBL
                  database translation. Note that the trailing terminator
                  character is removed before returning the translated protein

                  Note: if you set $dna_seq_obj->verbose(1) you will get a
                  warning if the first codon is not a valid initiator.

        Returns : A Bio::PrimarySeqI implementing object
        Args    : -terminator
                      character for terminator, default '*'
                      character for unknown, default 'X'
                      positive integer frame shift (in bases), default 0
                      integer codon table id, default 1
                      boolean, if true, complete CDS is expected. default false
                      boolean, if true, codons which are incomplete are translated if a
                      suitable amino acid is found. For instance, if the incomplete
                      codon is 'GG', the completed codon is 'GGN', which is glycine
                      (G). Defaults to 'false'; setting '-complete' also makes this
                      boolean, throw exception if ORF not complete, default false
                      if 'longest', find longest ORF.  other true value, find
                      first ORF.  default 0
                      optional L<Bio::Tools::CodonTable> object to use for
                      optional three-character string to force as initiation
                      codon (e.g. 'atg'). If unset, start codons are
                      determined by the CodonTable.  Case insensitive.
                      optional positive integer offset for fuzzy locations.
                      if set, must be either 1, 2, or 3


       The -start argument only applies when -orf is set to 1. By default all initiation codons
       found in the given codon table are used but when "start" is set to some codon this codon
       will be used exclusively as the initiation codon. Note that the default codon table (NCBI
       "Standard") has 3 initiation codons!

       By default translate() translates termination codons to the some character (default is *),
       both internal and trailing codons. Setting "-complete" to 1 tells translate() to remove
       the trailing character.

       -offset is used for seqfeatures which contain the the \codon_start tag and can be set to
       1, 2, or 3.  This is the offset by which the sequence translation starts relative to the
       first base of the feature

       For details on codon tables used by translate() see Bio::Tools::CodonTable.

       Deprecated argument set (v. 1.5.1 and prior versions) where each argument is an element in
       an array:

         1: character for terminator (optional), defaults to '*'.
         2: character for unknown amino acid (optional), defaults to 'X'.
         3: frame (optional), valid values are 0, 1, 2, defaults to 0.
         4: codon table id (optional), defaults to 1.
         5: complete coding sequence expected, defaults to 0 (false).
         6: boolean, throw exception if not complete coding sequence
            (true), defaults to warning (false)
         7: codontable, a custom Bio::Tools::CodonTable object (optional).

        Title   : transcribe
        Usage   : $xseq = $seq->transcribe
        Function: Convert base T to base U
        Returns : PrimarySeqI object of alphabet 'rna' or
                  undef if $seq->alphabet ne 'dna'
        Args    :

        Title   : rev_transcribe
        Usage   : $rtseq = $seq->rev_transcribe
        Function: Convert base U to base T
        Returns : PrimarySeqI object of alphabet 'dna' or
                  undef if $seq->alphabet ne 'rna'
        Args    :

        Title   : id
        Usage   : $id = $seq->id()
        Function: ID of the sequence. This should normally be (and actually is in
                  the implementation provided here) just a synonym for display_id().
        Returns : A string.
        Args    :

        Title   : length
        Usage   : $len = $seq->length()
        Returns : Integer representing the length of the sequence.
        Args    :

        Title   : desc
        Usage   : $seq->desc($newval);
                  $description = $seq->desc();
        Function: Get/set description text for a seq object
        Returns : Value of desc
        Args    : newvalue (optional)

        Title   : is_circular
        Usage   : if( $obj->is_circular) { /Do Something/ }
        Function: Returns true if the molecule is circular
        Returns : Boolean value
        Args    : none

Private functions

       These are some private functions for the PrimarySeqI interface. You do not need to
       implement these functions

        Title   : _find_orfs_nucleotide
        Usage   :
        Function: Finds ORF starting at 1st initiation codon in nucleotide sequence.
                  The ORF is not required to have a termination codon.
        Example :
        Returns : a list of string coordinates of ORF locations (0-based half-open),
                  sorted descending by length (so that the longest is first)
                  as: [ start, end, frame, length ], [ start, end, frame, length ], ...
        Args    : Nucleotide sequence,
                  CodonTable object,
                  (optional) alternative initiation codon (e.g. 'ATA'),
                  (optional) boolean that, if true, stops after finding the
                             first available ORF

        Title   : _attempt_to_load_Seq
        Usage   :
        Example :
        Returns :
        Args    :