Bio::Location Atomic
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Summary
Bio::Location::Atomic - Implementation of a Atomic Location on a Sequence
Package variables
No package variables defined.
Included modules
Bio::Location::WidestCoordPolicy
Inherit
Bio::LocationI Bio::Root::Root
Synopsis
    use Bio::Location::Atomic;
my $location = Bio::Location::Atomic->new(-start => 1, -end => 100, -strand => 1 ); if( $location->strand == -1 ) { printf "complement(%d..%d)\n", $location->start, $location->end; } else { printf "%d..%d\n", $location->start, $location->end; }
Description
This is an implementation of Bio::LocationI to manage simple location
information on a Sequence.
Methods
new
No description
Code
startDescriptionCode
endDescriptionCode
strandDescriptionCode
flip_strandDescriptionCode
seq_idDescriptionCode
lengthDescriptionCode
min_startDescriptionCode
max_startDescriptionCode
start_pos_typeDescriptionCode
min_endDescriptionCode
max_endDescriptionCode
end_pos_typeDescriptionCode
location_typeDescriptionCode
is_remoteDescriptionCode
each_LocationDescriptionCode
to_FTstringDescriptionCode
valid_LocationDescriptionCode
coordinate_policyDescriptionCode
truncDescriptionCode
Methods description
startcode    nextTop
  Title   : start
Usage : $start = $loc->start();
Function: get/set the start of this range
Returns : the start of this range
Args : optionaly allows the start to be set
: using $loc->start($start)
endcodeprevnextTop
  Title   : end
Usage : $end = $loc->end();
Function: get/set the end of this range
Returns : the end of this range
Args : optionaly allows the end to be set
: using $loc->end($start)
strandcodeprevnextTop
  Title   : strand
Usage : $strand = $loc->strand();
Function: get/set the strand of this range
Returns : the strandidness (-1, 0, +1)
Args : optionaly allows the strand to be set
: using $loc->strand($strand)
flip_strandcodeprevnextTop
  Title   : flip_strand
Usage : $location->flip_strand();
Function: Flip-flop a strand to the opposite
Returns : None
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
lengthcodeprevnextTop
 Title   : length
Usage : $len = $loc->length();
Function: get the length in the coordinate space this location spans
Example :
Returns : an integer
Args : none
min_startcodeprevnextTop
  Title   : min_start
Usage : my $minstart = $location->min_start();
Function: Get minimum starting location of feature startpoint
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 location of feature startpoint.
In this implementation this is exactly the same as min_start(). 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 (ie <,>, ^).
In this implementation this will always be 'EXACT'. Returns : type of position coded as text ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') Args : none
min_endcodeprevnextTop
  Title   : min_end
Usage : my $minend = $location->min_end();
Function: Get minimum ending location of feature endpoint
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 location of feature endpoint
In this implementation this is exactly the same as min_end(). 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 type (ie <,>, ^)
In this implementation this will always be 'EXACT'. Returns : type of position coded as text ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') Args : none
location_typecodeprevnextTop
  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
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
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 - for
Simple locations, the return value is just itself.
Args :
to_FTstringcodeprevnextTop
  Title   : to_FTstring
Usage : my $locstr = $location->to_FTstring()
Function: returns the FeatureTable string of this location
Returns : string
Args : none
valid_LocationcodeprevnextTop
 Title   : valid_Location
Usage : if ($location->valid_location) {...};
Function: boolean method to determine whether location is considered valid
(has minimum requirements for Simple implementation)
Returns : Boolean value: true if location is valid, false otherwise
Args : none
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
trunccodeprevnextTop
  Title   : trunc
Usage : $trunc_location = $location->trunc($start, $end, $relative_ori);
Function: To truncate a location and keep annotations and features
within the truncated segment intact.
This might do things differently where the truncation splits the location in half. CAVEAT : As yet, this is an untested and unannounced method. Use with caution! Returns : A Bio::Location::Atomic object.
Args : The start and end position for the trunction, and the relative
orientation.
Methods code
newdescriptionprevnextTop
sub new {
     my ($class, @args) = @_;
    $class = ref $class || $class;
    my $self = {};
    # This is for the case when we've done something like this
# get a 2 features from somewhere (like Bio::Tools::GFF)
# Do
# my $location = $f1->location->union($f2->location);
# We get an error without the following code which
# explictly loads the Bio::Location::Simple class
unless( $class->can('start') ) { eval { Bio::Root::Root->_load_module($class) }; if ( $@ ) { Bio::Root::Root->throw("$class cannot be found\nException $@"); } } bless $self,$class; my ($v,$start,$end,$strand,$seqid) = $self->_rearrange([qw(VERBOSE START END STRAND SEQ_ID)],@args); defined $v && $self->verbose($v); defined $strand && $self->strand($strand); defined $start && $self->start($start); defined $end && $self->end($end); if( defined $self->start && defined $self->end && $self->start > $self->end && $self->strand != -1 ) { $self->warn("When building a location, start ($start) is expected to be less than end ($end), ". "however it was not. Switching start and end and setting strand to -1"); $self->strand(-1); my $e = $self->end; my $s = $self->start; $self->start($e); $self->end($s); } $seqid && $self->seq_id($seqid); return $self;
}
startdescriptionprevnextTop
sub start {
  my ($self, $value) = @_;
  $self->min_start($value) if( defined $value );
  return $self->SUPER::start();
}
enddescriptionprevnextTop
sub end {
  my ($self, $value) = @_;

  $self->min_end($value) if( defined $value );
  return $self->SUPER::end();
}
stranddescriptionprevnextTop
sub strand {
  my $self = shift;

  if ( @_ ) {
       my $value = shift;
       if ( defined($value) ) {
	   if ( $value eq '+' ) { $value = 1; }
	   elsif ( $value eq '-' ) { $value = -1; }
	   elsif ( $value eq '.' ) { $value = 0; }
	   elsif ( $value != -1 && $value != 1 && $value != 0 ) {
	       $self->throw("$value is not a valid strand info");
	   }
           $self->{'_strand'} = $value;
       }
  }
  # do not pretend the strand has been set if in fact it wasn't
return $self->{'_strand'}; #return $self->{'_strand'} || 0;
}
flip_stranddescriptionprevnextTop
sub flip_strand {
    my $self= shift;
    $self->strand($self->strand * -1);
}
seq_iddescriptionprevnextTop
sub seq_id {
    my ($self, $seqid) = @_;
    if( defined $seqid ) {
	$self->{'_seqid'} = $seqid;
    }
    return $self->{'_seqid'};
}
lengthdescriptionprevnextTop
sub length {
   my ($self) = @_;
   return abs($self->end() - $self->start()) + 1;
}
min_startdescriptionprevnextTop
sub min_start {
    my ($self,$value) = @_;

    if(defined($value)) {
	$self->{'_start'} = $value;
    }
    return $self->{'_start'};
}
max_startdescriptionprevnextTop
sub max_start {
    my ($self,@args) = @_;
    return $self->min_start(@args);
}
start_pos_typedescriptionprevnextTop
sub start_pos_type {
    my($self) = @_;
    return 'EXACT';
}
min_enddescriptionprevnextTop
sub min_end {
    my($self,$value) = @_;

    if(defined($value)) {
	$self->{'_end'} = $value;
    }
    return $self->{'_end'};
}
max_enddescriptionprevnextTop
sub max_end {
    my($self,@args) = @_;
    return $self->min_end(@args);
}
end_pos_typedescriptionprevnextTop
sub end_pos_type {
    my($self) = @_;
    return 'EXACT';
}
location_typedescriptionprevnextTop
sub location_type {
    my ($self) = @_;
    return 'EXACT';
}
is_remotedescriptionprevnextTop
sub is_remote {
   my $self = shift;
   if( @_ ) {
       my $value = shift;
       $self->{'is_remote'} = $value;
   }
   return $self->{'is_remote'};
}
each_LocationdescriptionprevnextTop
sub each_Location {
   my ($self) = @_;
   return ($self);
}
to_FTstringdescriptionprevnextTop
sub to_FTstring {
     my($self) = @_;
    if( $self->start == $self->end ) {
	return $self->start;
    }
    my $str = $self->start . ".." . $self->end;
    if( $self->strand == -1 ) {
	$str = sprintf("complement(%s)", $str);
    }
    return $str;
}
valid_LocationdescriptionprevnextTop
sub valid_Location {
    my ($self) = @_;
    return 1 if $self->{'_start'} && $self->{'_end'};
    return 0;
}
coordinate_policydescriptionprevnextTop
sub coordinate_policy {
    my ($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 {
	    # called as class method
$coord_policy = $policy; } } return (ref($self) && exists($self->{'_coordpolicy'}) ? $self->{'_coordpolicy'} : $coord_policy);
}
truncdescriptionprevnextTop
sub trunc {
  my ($self,$start,$end,$relative_ori) = @_;

  my $newstart  = $self->start - $start+1;
  my $newend    = $self->end   - $start+1;
  my $newstrand = $relative_ori * $self->strand;

  my $out;
  if( $newstart < 1 || $newend > ($end-$start+1) ) {
    $out = Bio::Location::Atomic->new();
    $out->start($self->start);
    $out->end($self->end);
    $out->strand($self->strand);
    $out->seq_id($self->seqid);
    $out->is_remote(1);
  } else {
    $out = Bio::Location::Atomic->new();
    $out->start($newstart);
    $out->end($newend);
    $out->strand($newstrand);
    $out->seq_id();
  }

  return $out;
}

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 _