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
Carp
Inherit
Bio::RangeI
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
location_typeDescriptionCode
startDescriptionCode
endDescriptionCode
min_startDescriptionCode
max_startDescriptionCode
start_pos_typeDescriptionCode
flip_strandDescriptionCode
min_endDescriptionCode
max_endDescriptionCode
end_pos_typeDescriptionCode
seq_idDescriptionCode
is_remoteDescriptionCode
coordinate_policyDescriptionCode
to_FTstringDescriptionCode
each_LocationDescriptionCode
valid_LocationDescriptionCode
Methods description
location_typecode    nextTop
  Title   : location_type
Usage : my $location_type = $location->location_type();
Function: Get location type encoded as text
Returns : string ('EXACT', 'WITHIN', 'IN-BETWEEN')
Args : none
startcodeprevnextTop
  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
endcodeprevnextTop
  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
min_startcodeprevnextTop
  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
max_startcodeprevnextTop
  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
start_pos_typecodeprevnextTop
  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
flip_strandcodeprevnextTop
  Title   : flip_strand
Usage : $location->flip_strand();
Function: Flip-flop a strand to the opposite
Returns : None
Args : None
min_endcodeprevnextTop
  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
max_endcodeprevnextTop
  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
end_pos_typecodeprevnextTop
  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
seq_idcodeprevnextTop
  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
is_remotecodeprevnextTop
 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 AL445212.9:83662..166657 which can be found in GenBank/EMBL feature tables. Example : Returns : TRUE if the location is a remote location, and FALSE otherwise Args : Value to set to
coordinate_policycodeprevnextTop
  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
to_FTstringcodeprevnextTop
  Title   : to_FTstring
Usage : my $locstr = $location->to_FTstring()
Function: returns the FeatureTable string of this location
Returns : string
Args : none
each_LocationcodeprevnextTop
 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
valid_LocationcodeprevnextTop
 Title   : valid_Location
Usage : if ($location->valid_location) {...};
Function: boolean method to determine whether location is considered valid
(has minimum requirements for a specific LocationI implementation)
Returns : Boolean value: true if location is valid, false otherwise
Args : none
Methods code
location_typedescriptionprevnextTop
sub location_type {
     my ($self,@args) = @_;
    $self->throw_not_implemented();
}
startdescriptionprevnextTop
sub start {
    my ($self,@args) = @_;

    # throw if @args means that we don't support updating information
# in the interface but will delegate to the coordinate policy object
# for interpreting the 'start' value
$self->throw_not_implemented if @args; return $self->coordinate_policy()->start($self);
}
enddescriptionprevnextTop
sub end {
    my ($self,@args) = @_;

    # throw if @args means that we don't support updating information
# in the interface but will delegate to the coordinate policy object
# for interpreting the 'end' value
$self->throw_not_implemented if @args; return $self->coordinate_policy()->end($self);
}
min_startdescriptionprevnextTop
sub min_start {
    my($self) = @_;
    $self->throw_not_implemented();
}
max_startdescriptionprevnextTop
sub max_start {
    my($self) = @_;
    $self->throw_not_implemented();
}
start_pos_typedescriptionprevnextTop
sub start_pos_type {
    my($self) = @_;
    $self->throw_not_implemented();
}
flip_stranddescriptionprevnextTop
sub flip_strand {
    my $self= shift;
    $self->strand($self->strand * -1);
}
min_enddescriptionprevnextTop
sub min_end {
    my($self) = @_;
    $self->throw_not_implemented();
}
max_enddescriptionprevnextTop
sub max_end {
    my($self) = @_;
    $self->throw_not_implemented();
}
end_pos_typedescriptionprevnextTop
sub end_pos_type {
    my($self) = @_;
    $self->throw_not_implemented();
}
seq_iddescriptionprevnextTop
sub seq_id {
    my($self) = @_;
    $self->throw_not_implemented();
}
is_remotedescriptionprevnextTop
sub is_remote {
    shift->throw_not_implemented();
}
coordinate_policydescriptionprevnextTop
sub coordinate_policy {
    shift->throw_not_implemented();
}
to_FTstringdescriptionprevnextTop
sub to_FTstring {
     my($self) = @_;
    $self->throw_not_implemented();
}
each_LocationdescriptionprevnextTop
sub each_Location {
    my ($self,@args) = @_;
    $self->throw_not_implemented();
}
valid_LocationdescriptionprevnextTop
sub valid_Location {
    my ($self,@args) = @_;
    $self->throw_not_implemented();
}

1;
}
General documentation
FEEDBACKTop
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://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason StajichTop
Email jason-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _