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.AUTHOR
Lincoln Stein <[email protected]>.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.