/ 
bioperl-1.0
/ Bio::DB::GFF::Segment

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
Function: get the source sequence class
Returns : a string
Args    : none
Status  : Public

Returns 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.

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_stop

Title   : abs_stop
Usage   : $s->abs_stop
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()

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()

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.