Bio::Location Split
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Summary
Bio::Location::Split - Implementation of a Location on a Sequence
which has multiple locations (start/end points)
Package variables
No package variables defined.
Included modules
Bio::Root::Root
Inherit
Bio::Location::Atomic Bio::Location::SplitLocationI
Synopsis
    use Bio::Location::Split;
my $splitlocation = Bio::Location::Split->new(); $splitlocation->add_sub_Location(Bio::Location::Simple->new(-start=>1, -end=>30, -strand=>1)); $splitlocation->add_sub_Location(Bio::Location::Simple->new(-start=>50, -end=>61, -strand=>1)); my @sublocs = $splitlocation->sub_Location(); my $count = 1; # print the start/end points of the sub locations foreach my $location ( sort { $a->start <=> $b->start } @sublocs ) { printf "sub feature %d [%d..%d]\n", $count, $location->start,$location->end, "\n"; $count++; }
Description
This implementation handles locations which span more than one
start/end location, or and/or lie on different sequences, and can
work with split locations that depend on the specific order of the
sublocations ('join') or don't have a specific order but represent
a feature spanning noncontiguous sublocations ('order', 'bond').
Note that the order in which sublocations are added may be very important,
depending on the specific split location type. For instance, a 'join'
must have the sublocations added in the order that one expects to
join the sublocations, whereas all other types are sorted based on the
sequence location.
Methods
new
No description
Code
each_LocationDescriptionCode
sub_LocationDescriptionCode
add_sub_LocationDescriptionCode
splittypeDescriptionCode
is_single_sequenceDescriptionCode
guide_strandDescriptionCode
strandDescriptionCode
flip_strandDescriptionCode
startDescriptionCode
endDescriptionCode
min_startDescriptionCode
max_startDescriptionCode
start_pos_typeDescriptionCode
min_endDescriptionCode
max_endDescriptionCode
end_pos_typeDescriptionCode
seq_idDescriptionCode
to_FTstringDescriptionCode
Methods description
each_Locationcode    nextTop
 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()
sub_LocationcodeprevnextTop
 Title   : sub_Location
Usage : @sublocs = $splitloc->sub_Location();
Function: Returns the array of sublocations making up this compound (split)
location. Those sublocations referring to the same sequence as
the root split location will be sorted by start position (forward
sort) or end position (reverse sort) and come first (before
those on other sequences).
The sort order can be optionally specified or suppressed by the value of the first argument. The default is no sort. Returns : an array of Bio::LocationI implementing objects Args : Optionally 1, 0, or -1 for specifying a forward, no, or reverse sort order
add_sub_LocationcodeprevnextTop
 Title   : add_sub_Location
Usage : $splitloc->add_sub_Location(@locationIobjs);
Function: add an additional sublocation
Returns : number of current sub locations
Args : list of Bio::LocationI implementing object(s) to add
splittypecodeprevnextTop
  Title   : splittype
Usage : $splittype = $location->splittype();
Function: get/set the split splittype
Returns : the splittype of split feature (join, order)
Args : splittype to set
is_single_sequencecodeprevnextTop
  Title   : is_single_sequence
Usage : if($splitloc->is_single_sequence()) {
print "Location object $splitloc is split ".
"but only across a single sequence\n";
}
Function: Determine whether this location is split across a single or
multiple sequences.
This implementation ignores (sub-)locations that do not define seq_id(). The same holds true for the root location. Returns : TRUE if all sublocations lie on the same sequence as the root location (feature), and FALSE otherwise. Args : none
guide_strandcodeprevnextTop
  Title   : guide_strand
Usage : $str = $loc->guide_strand();
Function: Get/Set the guide strand. Of use only if the split type is
a 'join' (this helps determine the order of sublocation
retrieval)
Returns : value of guide strand (1, -1, or undef)
Args : new value (-1 or 1, optional)
strandcodeprevnextTop
 Title   : strand
Usage : $obj->strand($newval)
Function: For SplitLocations, setting the strand of the container
(this object) is a short-cut for setting the strand of all
sublocations.
In get-mode, checks if no sub-location is remote, and if all have the same strand. If so, it returns that shared strand value. Otherwise it returns undef. Example : Returns : on get, value of strand if identical between sublocations (-1, 1, or undef) Args : new value (-1 or 1, optional)
flip_strandcodeprevnextTop
  Title   : flip_strand
Usage : $location->flip_strand();
Function: Flip-flop a strand to the opposite. Also switch Split strand
from undef to -1 or -1 to undef
Returns : None
Args : None
startcodeprevnextTop
  Title   : start
Usage : $start = $location->start();
Function: get the starting point of the first (sorted) sublocation
Returns : integer
Args : none
endcodeprevnextTop
  Title   : end
Usage : $end = $location->end();
Function: get the ending point of the last (sorted) sublocation
Returns : integer
Args : none
min_startcodeprevnextTop
  Title   : min_start
Usage : $min_start = $location->min_start();
Function: get the minimum starting point
Returns : the minimum starting point from the contained sublocations
Args : none
max_startcodeprevnextTop
  Title   : max_start
Usage : my $maxstart = $location->max_start();
Function: Get maximum starting location of feature startpoint
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 <,>, ^)
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
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 <,>, ^)
Returns : type of position coded as text
('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
We override this here in order to propagate to all sublocations which are not remote (provided this root is not remote either) Returns : seq_id Args : [optional] seq_id value to set
to_FTstringcodeprevnextTop
  Title   : to_FTstring
Usage : my $locstr = $location->to_FTstring()
Function: returns the FeatureTable string of this location
Returns : string
Args : none
Methods code
newdescriptionprevnextTop
sub new {
    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
    # initialize
$self->{'_sublocations'} = []; my ( $type, $seqid, $locations ) = $self->_rearrange([qw(SPLITTYPE SEQ_ID LOCATIONS )], @args); if( defined $locations && ref($locations) =~ /array/i ) { $self->add_sub_Location(@$locations); } $seqid && $self->seq_id($seqid); $type ||= 'JOIN'; $type = lc ($type); $self->splittype($type); return $self;
}
each_LocationdescriptionprevnextTop
sub each_Location {
    my ($self, $order) = @_;
    my @locs = ();
    foreach my $subloc ($self->sub_Location($order)) {
	# Recursively check to get hierarchical split locations:
push @locs, $subloc->each_Location($order); } return @locs;
}
sub_LocationdescriptionprevnextTop
sub sub_Location {
    my ($self, $order) = @_;
    $order = 0 unless defined $order;
    if( defined($order) && ($order !~ /^-?\d+$/) ) {
	$self->throw("value $order passed in to sub_Location is $order, an invalid value");
    } 
    $order = 1 if($order > 1);
    $order = -1 if($order < -1);
    my @sublocs = defined $self->{'_sublocations'} ? @{$self->{'_sublocations'}} : ();

    # return the array if no ordering requested
return @sublocs if( ($order == 0) || (! @sublocs) ); # sort those locations that are on the same sequence as the top (`master')
# if the top seq is undefined, we take the first defined in a sublocation
my $seqid = $self->seq_id(); my $i = 0; while((! defined($seqid)) && ($i <= $#sublocs)) { $seqid = $sublocs[$i++]->seq_id(); } if((! $self->seq_id()) && $seqid) { $self->warn("sorted sublocation array requested but ". "root location doesn't define seq_id ". "(at least one sublocation does!)"); } my @locs = ($seqid ? grep { $_->seq_id() eq $seqid; } @sublocs : @sublocs); if(@locs) { if($order == 1) { # Schwartzian transforms for performance boost
@locs = map { $_->[0] } sort { (defined $a && defined $b) ? $a->[1] <=> $b->[1] : $a ? -1 : 1 } map { [$_, (defined $_->start ? $_->start : $_->end)] } @locs;; } else { # $order == -1
@locs = map { $_->[0]} sort { (defined $a && defined $b) ? $b->[1] <=> $a->[1] : $a ? -1 : 1 } map { [$_, (defined $_->end ? $_->end : $_->start)] } @locs; } } # push the rest unsorted
if($seqid) { push(@locs, grep { $_->seq_id() ne $seqid; } @sublocs); } # done!
return @locs;
}
add_sub_LocationdescriptionprevnextTop
sub add_sub_Location {
    my ($self,@args) = @_;
    my @locs;    
    foreach my $loc ( @args ) {
	if( !ref($loc) || ! $loc->isa('Bio::LocationI') ) {
	    $self->throw("Trying to add $loc as a sub Location but it doesn't implement Bio::LocationI!");
	    next;
	}	
	push @{$self->{'_sublocations'}}, $loc;
    }

    return scalar @{$self->{'_sublocations'}};
}
splittypedescriptionprevnextTop
sub splittype {
    my ($self, $value) = @_;
    if( defined $value || ! defined $self->{'_splittype'} ) {
	$value = 'JOIN' unless( defined $value );
	$self->{'_splittype'} = uc ($value);
    }
    return $self->{'_splittype'};
}
is_single_sequencedescriptionprevnextTop
sub is_single_sequence {
    my ($self) = @_;

    my $seqid = $self->seq_id();
    foreach my $loc ($self->sub_Location(0)) {
	$seqid = $loc->seq_id() if(! $seqid);
	if(defined($loc->seq_id()) && ($loc->seq_id() ne $seqid)) {
	    return 0;
	}
    }
    return 1;
}
guide_stranddescriptionprevnextTop
sub guide_strand {
	my $self = shift;
	return $self->{'strand'} = shift if @_;
	return $self->{'strand'};
}
stranddescriptionprevnextTop
sub strand {
    my ($self,$value) = @_;
    if( defined $value) {
		$self->{'strand'} = $value;
		# propagate to all sublocs
foreach my $loc ($self->sub_Location(0)) { $loc->strand($value); } } else { my ($strand, $lstrand); foreach my $loc ($self->sub_Location(0)) { # we give up upon any location that's remote or doesn't have
# the strand specified, or has a differing one set than
# previously seen.
# calling strand() is potentially expensive if the subloc is also
# a split location, so we cache it
$lstrand = $loc->strand(); if((! $lstrand) || ($strand && ($strand != $lstrand)) || $loc->is_remote()) { $strand = undef; last; } elsif(! $strand) { $strand = $lstrand; } } return $strand; }
}
flip_stranddescriptionprevnextTop
sub flip_strand {
    my $self = shift;
    for my $loc ( $self->sub_Location(0) ) {
		$loc->flip_strand;
		if ($loc->isa('Bio::Location::SplitLocationI')) {
			my $gs = ($self->guide_strand == -1) ? undef : -1;
			$loc->guide_strand($gs);
		}
    }
}
startdescriptionprevnextTop
sub start {
    my ($self,$value) = @_;    
    if( defined $value ) {
	$self->throw("Trying to set the starting point of a split location, ".
				 "that is not possible, try manipulating the sub Locations");
    }
    return $self->SUPER::start();
}
enddescriptionprevnextTop
sub end {
    my ($self,$value) = @_;    
    if( defined $value ) {
	$self->throw("Trying to set the ending point of a split location, ".
				 "that is not possible, try manipulating the sub Locations");
    }
    return $self->SUPER::end();
}
min_startdescriptionprevnextTop
sub min_start {
    my ($self, $value) = @_;    

    if( defined $value ) {
	$self->throw("Trying to set the minimum starting point of a split ".
				 "location, that is not possible, try manipulating the sub Locations");
    }
    my @locs = $self->sub_Location(1);
    return $locs[0]->min_start() if @locs; 
    return;
}
max_startdescriptionprevnextTop
sub max_start {
    my ($self,$value) = @_;

    if( defined $value ) {
	$self->throw("Trying to set the maximum starting point of a split ".
				 "location, that is not possible, try manipulating the sub Locations");
    }
    my @locs = $self->sub_Location(1);
    return $locs[0]->max_start() if @locs; 
    return;
}
start_pos_typedescriptionprevnextTop
sub start_pos_type {
    my ($self,$value) = @_;

    if( defined $value ) {
	$self->throw("Trying to set the start_pos_type of a split location, ".
				 "that is not possible, try manipulating the sub Locations");
    }
    my @locs = $self->sub_Location();
    return ( @locs ) ? $locs[0]->start_pos_type() : undef;
}
min_enddescriptionprevnextTop
sub min_end {
    my ($self,$value) = @_;

    if( defined $value ) {
	$self->throw("Trying to set the minimum end point of a split location, ".
				 "that is not possible, try manipulating the sub Locations");
    }
    # reverse sort locations by largest ending to smallest ending
my @locs = $self->sub_Location(-1); return $locs[0]->min_end() if @locs; return;
}
max_enddescriptionprevnextTop
sub max_end {
    my ($self,$value) = @_;

    if( defined $value ) {
	$self->throw("Trying to set the maximum end point of a split location, ".
				 "that is not possible, try manipulating the sub Locations");
    }
    # reverse sort locations by largest ending to smallest ending
my @locs = $self->sub_Location(-1); return $locs[0]->max_end() if @locs; return;
}
end_pos_typedescriptionprevnextTop
sub end_pos_type {
    my ($self,$value) = @_;

    if( defined $value ) {
	$self->throw("Trying to set end_pos_type of a split location, ".
				 "that is not possible, try manipulating the sub Locations");
    }
    my @locs = $self->sub_Location();
    return ( @locs ) ? $locs[0]->end_pos_type() : undef;
}
seq_iddescriptionprevnextTop
sub seq_id {
    my $self = shift;

    if(@_ && !$self->is_remote()) {
	foreach my $subloc ($self->sub_Location(0)) {
	    $subloc->seq_id(@_) if !$subloc->is_remote();
	}
    }
    return $self->SUPER::seq_id(@_);
}
to_FTstringdescriptionprevnextTop
sub to_FTstring {
    my ($self) = @_;
    my @strs;
	my $strand = $self->strand() || 0;
	my $stype = lc($self->splittype());
	my $guide = $self->guide_strand();

    if( $strand < 0 ) {
		$self->flip_strand; # this will recursively set the strand
# to +1 for all the sub locations
} # If the split type is join, the order is important;
# otherwise must be 5'->3' regardless
my @locs = ($stype eq 'join' && (!$guide && $strand == -1)) ? reverse $self->sub_Location() : $self->sub_Location() ; foreach my $loc ( @locs ) { $loc->verbose($self->verbose); my $str = $loc->to_FTstring(); # we only append the remote seq_id if it hasn't been done already
# by the sub-location (which it should if it knows it's remote)
# (and of course only if it's necessary)
if( (! $loc->is_remote) && defined($self->seq_id) && defined($loc->seq_id) && ($loc->seq_id ne $self->seq_id) ) { $str = sprintf("%s:%s", $loc->seq_id, $str); } push @strs, $str; } $self->flip_strand if $strand < 0; my $str; if( @strs == 1 ) { ($str) = @strs; } elsif( @strs == 0 ) { $self->warn("no Sublocations for this splitloc, so not returning anything\n"); } else { $str = sprintf("%s(%s)",lc $self->splittype, join(",", @strs)); } if( $strand < 0 ) { # wrap this in a complement if it was unrolled
$str = sprintf("%s(%s)",'complement',$str); } return $str;
}
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 _
LocationI methodsTop
coordinate_policyTop
  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 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.
valid_LocationTop
 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