Bio::Map Relative
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Bio::Map::Relative - Represents what a Position's coordiantes are relative to.
Package variables
No package variables defined.
Included modules
Scalar::Util qw ( looks_like_number )
Bio::Map::RelativeI Bio::Root::Root
    # Get a Bio::Map::PositionI somehow
my $pos = Bio::Map::Position->new(-value => 100);
# its co-ordinates are implicitly relative to the start of its map my $implicit_relative = $pos->relative; my $type = $implicit_relative->type; # $type eq 'map' my $value = $implicit_relative->$type(); # $value == 0 # make its co-ordinates relative to another Position my $pos_we_are_relative_to = Bio::Map::Position->new(-value => 200); my $relative = Bio::Map::Relative->new(-position => $pos_we_are_relative_to); $pos->relative($relative); # Get the start co-ordinate of $pos relative to $pos_we_are_relative_to my $start = $pos->start; # $start == 100 # Get the start co-ordinate of $pos relative to the start of the map my $abs_start = $relative->absolute_conversion($pos); # $abs_start == 300 # - or - $pos->absolute(1); my $abs_start = $pos->start; # $abs_start == 300 $pos->absolute(0); # Get the start co-ordinate of $pos relative to a third Position my $pos_frame_of_reference = Bio::Map::Position->new(-value => 10); my $relative2 = Bio::Map::Relative->new(-position => $pos_frame_of_reference); my $start = $pos->start($relative2); # $start == 290
A Relative object is used to describe what the co-ordinates (numerical(),
start(), end()) of a Position are relative to. By default they are
implicitly assumed to be relative to the start of the map the Position is on.
But setting the relative() of a Position to one of these objects lets us
define otherwise.
Methods description
newcode    nextTop
 Title   : new
Usage : my $relative = Bio::Map::Relative->new();
Function: Build a new Bio::Map::Relative object.
Returns : Bio::Map::Relative object
Args : -map => int : coordinates are relative to this point on the
Position's map [default is map => 0, ie.
relative to the start of the map],
-element => Mappable : or relative to this element's (a
Bio::Map::MappableI) position in the map
(only works if the given element has only one
position in the map the Position belongs to),
-position => Position : or relative to this other Position (a
Bio::Map::PositionI, fails if the other
Position is on a different map to this map)
-description => string: Free text description of what this relative describes (To say a Position is relative to something and upstream of it, the Position's start() co-ordinate should be set negative)
 Title   : absolute_conversion
Usage : my $absolute_coord = $relative->absolute_conversion($pos);
Function: Convert the start co-ordinate of the supplied position into a number
relative to the start of its map.
Returns : scalar number
Args : Bio::Map::PositionI object
 Title   : type
Usage : my $type = $relative->type();
Function: Get the type of thing we are relative to. The types correspond
to a method name, so the value of what we are relative to can
subsequently be found by $value = $relative->$type;
Note that type is set by the last method that was set, or during new(). Returns : the string 'map', 'element' or 'position', or undef Args : none
 Title   : map
Usage : my $int = $relative->map();
Function: Get/set the distance from the start of the map that the Position's
co-ordiantes are relative to.
Returns : int
Args : none to get, OR
int to set; a value of 0 means relative to the start of the map.
 Title   : element
Usage : my $element = $relative->element();
Function: Get/set the map element (Mappable) the Position is relative to. If
the Mappable has more than one Position on the Position's map, we
will be relative to the Mappable's first Position on the map.
Returns : Bio::Map::MappableI
Args : none to get, OR
Bio::Map::MappableI to set
 Title   : position
Usage : my $position = $relative->position();
Function: Get/set the Position your Position is relative to. Your Position
will be made relative to the start of this supplied Position. It
makes no difference what maps the Positions are on.
Returns : Bio::Map::PositionI
Args : none to get, OR
Bio::Map::PositionI to set
 Title   : description
Usage : my $description = $relative->description();
Function: Get/set a textual description of what this relative describes.
Returns : string
Args : none to get, OR
string to set
Methods code
sub new {
    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
    my ($map, $element, $position, $desc) = 
	$self->_rearrange([qw( MAP ELEMENT POSITION DESCRIPTION )], @args);
    if (defined($map) + defined($element) + defined($position) > 1) {
        $self->throw("-map, -element and -position are mutually exclusive");
    defined($map) && $self->map($map);
    $element && $self->element($element);
    $position && $self->position($position);
    $desc && $self->description($desc);
    return $self;
sub absolute_conversion {
    my ($self, $pos) = @_;
    $self->throw("Must supply an object") unless ref($pos);
    $self->throw("This is [$pos], not a Bio::Map::PositionI") unless $pos->isa('Bio::Map::PositionI');
    # get the raw start position of our position
my $prior_abs = $pos->absolute; $pos->absolute(0) if $prior_abs; my $raw = $pos->start; $pos->absolute($prior_abs) if $prior_abs; $self->throw("Can't convert co-ordinates when start isn't set") unless defined($raw); #*** needed? return undef?
# what are we relative to?
my $type = $self->type; my $value = $self->$type; $self->throw("Details not yet set for this Relative, cannot convert") unless $type && defined($value); # get the absolute start of the thing we're relative to
my $map = $pos->map; if ($type eq 'element') { $self->throw("Relative to a Mappable, but the Position has no map") unless $map; my @positions = $value->get_positions($map); $value = shift(@positions); $self->throw("Relative to a Mappable, but this Mappable has no positions on the supplied Position's map") unless $value; } if (ref($value)) { # psuedo-recurse
my $rel = $value->relative; $value = $rel->absolute_conversion($value); } if (defined($value)) { return $value + $raw; } return;
sub type {
    my $self = shift;
    return $self->{_use} || return;
sub map {
    my ($self, $num) = @_;
    if (defined($num)) {
        $self->throw("This is [$num], not a number") unless looks_like_number($num);
        $self->{_use} = 'map';
        $self->{_map} = $num;
    return defined($self->{_map}) ? $self->{_map} : return;
sub element {
    my ($self, $element) = @_;
    if ($element) {
        $self->throw("Must supply an object") unless ref($element);
        $self->throw("This is [$element], not a Bio::Map::MappableI") unless $element->isa('Bio::Map::MappableI');
        $self->{_use} = 'element';
        $self->{_element} = $element;
    return $self->{_element} || return;
sub position {
    my ($self, $pos) = @_;
    if ($pos) {
        $self->throw("Must supply an object") unless ref($pos);
        $self->throw("This is [$pos], not a Bio::Map::PositionI") unless $pos->isa('Bio::Map::PositionI');
        $self->{_use} = 'position';
        $self->{_position} = $pos;
    return $self->{_position} || return;
sub description {
    my $self = shift;
    if (@_) { $self->{desc} = shift }
    return $self->{desc} || '';

General documentation
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AUTHOR - Sendu BalaTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _