Bio::DB::GFF::Segment -- Simple DNA segment object See Bio::DB::GFF. 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. 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 string Args : none Status : Public Returns the sequence for this segment as a simple string. (-) strand segments are automatically reverse complemented This method is also called dna() and protein() for backward compatibility with AceDB.

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. 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 Report them please. bioperl 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. Jason Stajich <jason@bioperl.org>.