Bio::DB::GFF::Segment(3)

NAME
Bio::DB::GFF::Segment -- Simple DNA segment object

SYNOPSIS
See Bio::DB::GFF.

DESCRIPTION
Bio::DB::GFF::Segment provides the basic representation of a range of DNA contained in a GFF database. It is the base class from which the Bio::DB::GFF::RelSegment and Bio::DB::GFF::Feature classes are derived.

Generally, you will not create or manipulate Bio::DB::GFF::Segment objects directly, but use those that are returned by the Bio::DB::GFF module.

API
The remainder of this document describes the API for Bio::DB::GFF::Segment.

  new
 Title   : new
 Usage   : $s = Bio::DB::GFF::Segment->new(@args)
 Function: create a new segment
 Returns : a new Bio::DB::GFF::Segment object
 Args    : see below
 Status  : Public

This method creates a new Bio::DB::GFF::Segment object. Generally this is called automatically by the Bio::DB::GFF module and derivatives.

There are five positional arguments:

 $factory      a Bio::DB::GFF::Adaptor to use for database access
 $sourceseq    ID of the source sequence
 $sourceclass  class of the source sequence
 $start        start of the desired segment relative to source sequence
 $stop         stop of the desired segment relative to source sequence

  factory
 Title   : factory
 Usage   : $s->factory
 Function: get the factory object
 Returns : a Bio::DB::GFF::Adaptor
 Args    : none
 Status  : Public

This is a read-only accessor for the Bio::DB::GFF::Adaptor object used to create the segment.

  start
 Title   : start
 Usage   : $s->start
 Function: start of segment
 Returns : integer
 Args    : none
 Status  : Public

This is a read-only accessor for the start of the segment.

  end
 Title   : end
 Usage   : $s->end
 Function: end of segment
 Returns : integer
 Args    : none
 Status  : Public

This is a read-only accessor for the end of the segment.

  stop
 Title   : stop
 Usage   : $s->stop
 Function: stop of segment
 Returns : integer
 Args    : none
 Status  : Public

This is an alias for end(), provided for AcePerl compatibility.

  length
 Title   : length
 Usage   : $s->length
 Function: length of segment
 Returns : integer
 Args    : none
 Status  : Public

Returns the length of the segment. Always a positive number.

  strand
 Title   : strand
 Usage   : $s->strand
 Function: strand of segment
 Returns : +1,0,-1
 Args    : none
 Status  : Public

Returns the strand on which the segment resides, either +1, 0 or -1.

  low
 Title   : low
 Usage   : $s->low
 Function: return lower coordinate
 Returns : lower coordinate
 Args    : none
 Status  : Public

Returns the lower coordinate, either start or end.

  high
 Title   : high
 Usage   : $s->high
 Function: return higher coordinate
 Returns : higher coordinate
 Args    : none
 Status  : Public

Returns the higher coordinate, either start or end.

  sourceseq
 Title   : sourceseq
 Usage   : $s->sourceseq
 Function: get the segment source
 Returns : a string
 Args    : none
 Status  : Public

Returns the name of the source sequence for this segment.

  class
 Title   : class
 Usage   : $s->class([$newclass])
 Function: get the source sequence class
 Returns : a string
 Args    : new class (optional)
 Status  : Public

Gets or sets the class for the source sequence for this segment.

  subseq
 Title   : subseq
 Usage   : $s->subseq($start,$stop)
 Function: generate a subsequence
 Returns : a Bio::DB::GFF::Segment object
 Args    : start and end of subsequence
 Status  : Public

This method generates a new segment from the start and end positions given in the arguments. If stop < start, then the strand is reversed.

  seq
 Title   : seq
 Usage   : $s->seq
 Function: get the sequence string for this segment
 Returns : a Bio::PrimarySeq
 Args    : none
 Status  : Public

Returns the sequence for this segment as a Bio::PrimarySeq. (-) strand segments are automatically reverse complemented

The method is called dna() return the data as a simple sequence string.

  dna
 Title   : dna
 Usage   : $s->dna
 Function: get the DNA string for this segment
 Returns : a string
 Args    : none
 Status  : Public

Returns the sequence for this segment as a simple string. (-) strand segments are automatically reverse complemented

The method is also called protein().

  primary_seq
 Title   : primary_seq
 Usage   : $s->primary_seq
 Function: returns a Bio::PrimarySeqI compatible object
 Returns : a Bio::PrimarySeqI object
 Args    : none
 Status  : Public

This is for compatibility with BioPerl's separation of SeqI from PrimarySeqI. It just returns itself.

  type
 Title   : type
 Usage   : $s->type
 Function: return the string "feature"
 Returns : the string "feature"
 Args    : none
 Status  : Public

This is for future sequence ontology-compatibility and represents the default type of a feature on the genome

  equals
 Title   : equals
 Usage   : $s->equals($d)
 Function: segment equality
 Returns : true, if two segments are equal
 Args    : another segment
 Status  : Public

Returns true if the two segments have the same source sequence, start and stop.

  asString
 Title   : asString
 Usage   : $s->asString
 Function: human-readable string for segment
 Returns : a string
 Args    : none
 Status  : Public

Returns a human-readable string representing this sequence. Format is:

   sourceseq/start,stop

  clone
 Title   : clone
 Usage   : $copy = $s->clone
 Function: make a copy of this segment
 Returns : a Bio::DB::GFF::Segment object
 Args    : none
 Status  : Public

This method creates a copy of the segment and returns it.

  error
 Title   : error
 Usage   : $error = $s->error([$new_error])
 Function: get or set the last error
 Returns : a string
 Args    : an error message (optional)
 Status  : Public

In case of a fault, this method can be used to obtain the last error message. Internally it is called to set the error message.

Relative Addressing Methods
The following methods are provided for compatibility with Bio::DB::GFF::RelSegment, which provides relative addressing functions.

  abs_start
 Title   : abs_start
 Usage   : $s->abs_start
 Function: the absolute start of the segment
 Returns : an integer
 Args    : none
 Status  : Public

This is an alias to start(), and provided for API compatibility with Bio::DB::GFF::RelSegment.

  abs_end
 Title   : abs_end
 Usage   : $s->abs_end
 Function: the absolute stop of the segment
 Returns : an integer
 Args    : none
 Status  : Public

This is an alias to stop(), and provided for API compatibility with Bio::DB::GFF::RelSegment.

  abs_strand
 Title   : abs_strand
 Usage   : $s->abs_strand
 Function: the absolute strand of the segment
 Returns : +1,0,-1
 Args    : none
 Status  : Public

This is an alias to strand(), and provided for API compatibility with Bio::DB::GFF::RelSegment.

  abs_ref
 Title   : abs_ref
 Usage   : $s->abs_ref
 Function: the reference sequence for this segment
 Returns : a string
 Args    : none
 Status  : Public

This is an alias to sourceseq(), and is here to provide API compatibility with Bio::DB::GFF::RelSegment.

  refseq
 Title   : refseq
 Usage   : $s->refseq
 Function: get or set the reference sequence
 Returns : a string
 Args    : none
 Status  : Public

Examine or change the reference sequence. This is an alias to sourceseq(), provided here for API compatibility with Bio::DB::GFF::RelSegment.

  ref
 Title   : ref
 Usage   : $s->refseq
 Function: get or set the reference sequence
 Returns : a string
 Args    : none
 Status  : Public

An alias for refseq()

  seq_id
 Title   : seq_id
 Usage   : $ref = $s->seq_id
 Function: get the reference sequence in a LocationI-compatible way
 Returns : a string
 Args    : none
 Status  : Public

An alias for refseq() but only allows reading.

  truncated
 Title   : truncated
 Usage   : $truncated = $s->truncated
 Function: Flag indicating that the segment was truncated during creation
 Returns : A boolean flag
 Args    : none
 Status  : Public

This indicates that the sequence was truncated during creation. The returned flag is undef if no truncation occured. If truncation did occur, the flag is actually an array ref in which the first element is true if truncation occurred on the left, and the second element occurred if truncation occurred on the right.

  Bio::RangeI Methods
The following Bio::RangeI methods are supported:

overlaps(), contains(), equals(),intersection(),union(),overlap_extent()

  Bio::SeqI implementation

  primary_id
 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

  display_name
 Title   : display_name
 Usage   : $id = $obj->display_name or $obj->display_name($newid);
 Function: Gets or sets the display id, also known as the common name of
           the Seq object.

           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 LOCUS
           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 issues.
 Returns : A string
 Args    : None or a new id

Note, this used to be called display_id(), and this name is preserved for backward compatibility. The default is to return the seq_id().

  accession_number
 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
           "unknown".
 Returns : A string
 Args    : None

  alphabet
 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 type - if there is no type specified it
           has to guess.
 Args    : none
 Status  : Virtual

  desc
 Title   : desc
 Usage   : $seqobj->desc($string) or $seqobj->desc()
 Function: Sets or gets the description of the sequence
 Example :
 Returns : The description
 Args    : The description or none

  species
 Title   : species
 Usage   : $species = $seq->species() or $seq->species($species)
 Function: Gets or sets the species
 Example :
 Returns : Bio::Species object
 Args    : None or Bio::Species object

See Bio::Species for more information

  annotation
 Title   : annotation
 Usage   : $ann = $seq->annotation or $seq->annotation($annotation)
 Function: Gets or sets the annotation
 Example :
 Returns : Bio::Annotation object
 Args    : None or Bio::Annotation object

See Bio::Annotation for more information

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

BUGS
Report them please.

SEE ALSO
bioperl

AUTHOR
Lincoln Stein <lstein@cshl.org>.

Copyright (c) 2001 Cold Spring Harbor Laboratory.

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

CONTRIBUTORS
Jason Stajich <jason@bioperl.org>.