Bio
LocationI
Summary
Bio::LocationI - Abstract interface of a Location on a Sequence
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
# get a LocationI somehow
printf( "start = %d, end = %d, strand = %s, seq_id = %s\n",
$location->start, $location->end, $location->strand,
$location->seq_id);
print "location str is ", $location->to_FTstring(), "\n";
Description
This Interface defines the methods for a Bio::LocationI, an object
which encapsulates a location on a biological sequence. Locations
need not be attached to actual sequences as they are stand alone
objects. LocationI objects are used by
Bio::SeqFeatureI objects to
manage and represent locations for a Sequence Feature.
Methods
Methods description
Title : location_type
Usage : my $location_type = $location->location_type();
Function: Get location type encoded as text
Returns : string ('EXACT', 'WITHIN', 'BETWEEN')
Args : none |
Title : start
Usage : $start = $location->start();
Function: Get the start coordinate of this location as defined by the
currently active coordinate computation policy. In simple cases,
this will return the same number as min_start() and max_start(),
in more ambiguous cases like fuzzy locations the number may be
equal to one or neither of both.
We override this here from RangeI in order to delegate
'get' to a Bio::Location::CoordinatePolicy implementing
object. Implementing classes may also wish to provide
'set' functionality, in which case they *must* override
this method. The implementation provided here will throw
an exception if called with arguments.
Returns : A positive integer value.
Args : none |
Title : end
Usage : $end = $location->end();
Function: Get the end coordinate of this location as defined by the
currently active coordinate computation policy. In simple cases,
this will return the same number as min_end() and max_end(),
in more ambiguous cases like fuzzy locations the number may be
equal to one or neither of both.
We override this here from Bio::RangeI in order to delegate
'get' to a Bio::Location::CoordinatePolicy implementing
object. Implementing classes may also wish to provide
'set' functionality, in which case they *must* override
this method. The implementation provided here will throw
an exception if called with arguments.
Returns : A positive integer value.
Args : none |
Title : min_start
Usage : my $minstart = $location->min_start();
Function: Get minimum starting point of feature.
Note that an implementation must not call start() in this method.
Returns : integer or undef if no minimum starting point.
Args : none |
Title : max_start
Usage : my $maxstart = $location->max_start();
Function: Get maximum starting point of feature.
Note that an implementation must not call start() in this method
unless start() is overridden such as not to delegate to the
coordinate computation policy object.
Returns : integer or undef if no maximum starting point.
Args : none |
Title : start_pos_type
Usage : my $start_pos_type = $location->start_pos_type();
Function: Get start position type encoded as text
Known valid values are 'BEFORE' (<5..100), 'AFTER' (>5..100),
'EXACT' (5..100), 'WITHIN' ((5.10)..100), 'BETWEEN', (5^6), with
their meaning best explained by their GenBank/EMBL location string
encoding in brackets.
Returns : string ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
Args : none |
Title : min_end
Usage : my $minend = $location->min_end();
Function: Get minimum ending point of feature.
Note that an implementation must not call end() in this method
unless end() is overridden such as not to delegate to the
coordinate computation policy object.
Returns : integer or undef if no minimum ending point.
Args : none |
Title : max_end
Usage : my $maxend = $location->max_end();
Function: Get maximum ending point of feature.
Note that an implementation must not call end() in this method
unless end() is overridden such as not to delegate to the
coordinate computation policy object.
Returns : integer or undef if no maximum ending point.
Args : none |
Title : end_pos_type
Usage : my $end_pos_type = $location->end_pos_type();
Function: Get end position encoded as text.
Known valid values are 'BEFORE' (5..<100), 'AFTER' (5..>100),
'EXACT' (5..100), 'WITHIN' (5..(90.100)), 'BETWEEN', (5^6), with
their meaning best explained by their GenBank/EMBL location string
encoding in brackets.
Returns : string ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
Args : none |
Title : seq_id
Usage : my $seqid = $location->seq_id();
Function: Get/Set seq_id that location refers to
Returns : seq_id (a string)
Args : [optional] seq_id value to set |
Title : coordinate_policy
Usage : $policy = $location->coordinate_policy();
$location->coordinate_policy($mypolicy); # set may not be possible
Function: Get the coordinate computing policy employed by this object.
See Bio::Location::CoordinatePolicyI for documentation about
the policy object and its use.
The interface *does not* require implementing classes to accept
setting of a different policy. The implementation provided here
does, however, allow to do so.
Implementors of this interface are expected to initialize
every new instance with a
Bio::Location::CoordinatePolicyI object. The
implementation provided here will return a default policy
object if none has been set yet. To change this default
policy object call this method as a class method with an
appropriate argument. Note that in this case only
subsequently created Location objects will be affected.
Returns : A Bio::Location::CoordinatePolicyI implementing object.
Args : On set, a Bio::Location::CoordinatePolicyI implementing object. |
Title : to_FTstring
Usage : my $locstr = $location->to_FTstring()
Function: returns the FeatureTable string of this location
Returns : string
Args : none |
Methods code
sub location_type
{ my ($self,@args) = @_;
$self->throw_not_implemented();} | sub start
{ my ($self,@args) = @_;
$self->throw_not_implemented if @args;
return $self->coordinate_policy()->start($self);} | sub end
{ my ($self,@args) = @_;
$self->throw_not_implemented if @args;
return $self->coordinate_policy()->end($self);} | sub min_start
{ my($self) = @_;
$self->throw_not_implemented();} | sub max_start
{ my($self) = @_;
$self->throw_not_implemented();} | sub start_pos_type
{ my($self) = @_;
$self->throw_not_implemented();} | sub min_end
{ my($self) = @_;
$self->throw_not_implemented();} | sub max_end
{ my($self) = @_;
$self->throw_not_implemented();} | sub end_pos_type
{ my($self) = @_;
$self->throw_not_implemented();} | sub seq_id
{ my ($self, $seqid) = @_;
if( defined $seqid ) {
$self->{'_seqid'} = $seqid;
}
return $self->{'_seqid'};} | sub coordinate_policy
{ my ($self, $policy) = @_;
if(defined($policy)) {
if(! $policy->isa('Bio::Location::CoordinatePolicyI')) {
$self->throw("Object of class ".ref($policy)." does not implement".
" Bio::Location::CoordinatePolicyI");
}
if(ref($self)) {
$self->{'_coordpolicy'} = $policy;
} else {
$coord_policy = $policy;
}
}
return (ref($self) && exists($self->{'_coordpolicy'}) ?
$self->{'_coordpolicy'} : $coord_policy);} | sub to_FTstring
{ my($self) = @_;
$self->throw_not_implemented();} | General documentation
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
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bioperl-l@bioperl.org - General discussion
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Report bugs to the Bioperl bug tracking system to help us keep track
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http://bio.perl.org/bioperl-bugs/
| AUTHOR - Jason Stajich | Top |
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _