Bio::Location
Split
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
Inherit
Synopsis
use Bio::Location::Split;
my $splitlocation = new Bio::Location::Split();
$splitlocation->add_sub_Location(new Bio::Location::Simple(-start=>1,
-end=>30,
-strand=>1));
$splitlocation->add_sub_Location(new Bio::Location::Simple(-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.
Methods
Methods description
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 a forward sort.
Returns : an array of Bio::LocationI implementing objects
Args : Optionally 1, 0, or -1 for specifying a forward, no, or reverse
sort order |
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 |
Title : splittype
Usage : $splittype = $fuzzy->splittype();
Function: get/set the split splittype
Returns : the splittype of split feature (join, order)
Args : splittype to set |
Title : is_single_sequence
Usage : if($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 |
Title : start
Usage : $start = $location->start();
Function: get the starting point of the first (sorted) sublocation
Returns : integer
Args : none |
Title : end
Usage : $end = $location->end();
Function: get the ending point of the last (sorted) sublocation
Returns : integer
Args : none |
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 |
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 |
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 |
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 |
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 |
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 |
Title : to_FTstring
Usage : my $locstr = $location->to_FTstring()
Function: returns the FeatureTable string of this location
Returns : string
Args : none |
Methods code
BEGIN {
@CORBALOCATIONOPERATOR= ('NONE','JOIN', undef, 'ORDER'); } | sub new
{ my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
$self->{'_sublocations'} = [];
my ( $type, $locations ) = $self->_rearrange([qw(SPLITTYPE
LOCATIONS)], @args);
if( defined $locations && ref($locations) =~ /array/i ) {
$self->add_sub_Location(@$locations);
}
$type = lc ($type);
$self->splittype($type || 'JOIN');
return $self;} | sub sub_Location
{ my ($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 @sublocs if( ($order == 0) || (! @sublocs) );
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) {
@locs = map {$_->[0]}
sort { $a->[1] <=> $b->[1] }
map { [$_=>$_->start] } @locs;
} else {
@locs = map {$_->[0]}
sort { $b->[1] <=> $a->[1] }
map { [$_=>$_->end] } @locs;
}
}
if($seqid) {
push(@locs, grep { $_->seq_id() ne $seqid; } @sublocs);
}
return @locs;} | sub add_sub_Location
{ my ($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'}};} | sub splittype
{ my ($self, $value) = @_;
if( defined $value || ! defined $self->{'_splittype'} ) {
$value = 'JOIN' unless( defined $value );
$self->{'_splittype'} = uc ($value);
}
return $self->{'_splittype'};} | sub is_single_sequence
{ my ($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 $seqid)) {
return 0;
}
}
return 1;} | sub start
{ my ($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 $self->SUPER::start();} | sub end
{ my ($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 $self->SUPER::end();} | sub min_start
{ my ($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 $locs[0]->min_start() if @locs;
return undef;} | sub max_start
{ my ($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 $locs[0]->max_start() if @locs;
return undef;} | sub start_pos_type
{ my ($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 ) ? $locs[0]->start_pos_type() : undef;} | sub min_end
{ my ($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");
}
my @locs = $self->sub_Location(-1);
return $locs[0]->min_end() if @locs;
return undef;} | sub max_end
{ my ($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");
}
my @locs = $self->sub_Location(-1);
return $locs[0]->max_end() if @locs;
return undef;} | sub end_pos_type
{ my ($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 ) ? $locs[0]->end_pos_type() : undef;} | sub to_FTstring
{ my ($self) = @_;
my @strs;
foreach my $loc ( $self->sub_Location() ) {
my $str = $loc->to_FTstring();
if( 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;
}
my $str = sprintf("%s(%s)",lc $self->splittype, join(",", @strs));
return $str;} | 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
the bugs and their resolution. Bug reports can be submitted via email
or the web:
bioperl-bugs@bio.perl.org
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 _
Title : seq_id
Usage : my $seqid = $location->seq_id();
Function: Get/Set seq_id that location refers to
Returns : seq_id
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 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.