Bio
LocationI
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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 : 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.
See Bio::Location::CoordinatePolicyI for more information |
Title : each_Location
Usage : @locations = $locObject->each_Location($order);
Function: Conserved function call across Location:: modules - will
return an array containing the component Location(s) in
that object, regardless if the calling object is itself a
single location or one containing sublocations.
Returns : an array of Bio::LocationI implementing objects
Args : Optional sort order to be passed to sub_Location() for Splits |
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
See Bio::Location::CoordinatePolicy and Bio::RangeI for more
information |
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 : is_remote
Usage : $is_remote_loc = $loc->is_remote()
Function: Whether or not a location is a remote location.
A location is said to be remote if it is on a different
'object' than the object which 'has' this
location. Typically, features on a sequence will sometimes
have a remote location, which means that the location of
the feature is on a different sequence than the one that is
attached to the feature. In such a case, $loc->seq_id will
be different from $feat->seq_id (usually they will be the
same).
While this may sound weird, it reflects the location of the
kind of AB18375:450-900 which can be found in GenBank/EMBL
feature tables.
Example :
Returns : TRUE if the location is a remote location, and FALSE otherwise
Args : |
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 : 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 : 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 : 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 : 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 : 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 : 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
See Bio::Location::CoordinatePolicy for more information |
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 : to_FTstring
Usage : my $locstr = $location->to_FTstring()
Function: returns the FeatureTable string of this location
Returns : string
Args : none |
Methods code
sub coordinate_policy
{ my ($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'} : $coord_policy);} | sub each_Location
{ my ($self,@args) = @_;
$self->throw_not_implemented();
}
1;} | sub end
{ my ($self,@args) = @_;
$self->throw_not_implemented if @args;
return $self->coordinate_policy()->end($self);} | sub end_pos_type
{ my($self) = @_;
$self->throw_not_implemented();} | sub is_remote
{ shift->throw_not_implemented(); } | sub location_type
{ my ($self,@args) = @_;
$self->throw_not_implemented();} | sub max_end
{ my($self) = @_;
$self->throw_not_implemented();} | sub max_start
{ my($self) = @_;
$self->throw_not_implemented();} | sub min_end
{ my($self) = @_;
$self->throw_not_implemented();} | sub min_start
{ my($self) = @_;
$self->throw_not_implemented();} | sub seq_id
{ my ($self, $seqid) = @_;
if( defined $seqid ) {
$self->{'_seqid'} = $seqid;
}
return $self->{'_seqid'};} | sub start
{ my ($self,@args) = @_;
$self->throw_not_implemented if @args;
return $self->coordinate_policy()->start($self);} | sub start_pos_type
{ my($self) = @_;
$self->throw_not_implemented();} | sub to_FTstring
{ my($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
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bio.perl.org/MailList.html - About the mailing lists
Report bugs to the Bioperl bug tracking system to help us keep track
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bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
| AUTHOR - Jason Stajich | Top |
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _