Bio::Map Relative
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Summary
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 )
Inherit
Bio::Map::RelativeI Bio::Root::Root
Synopsis
    # 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
Description
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
newDescriptionCode
absolute_conversionDescriptionCode
typeDescriptionCode
mapDescriptionCode
elementDescriptionCode
positionDescriptionCode
descriptionDescriptionCode
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)
absolute_conversioncodeprevnextTop
 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
typecodeprevnextTop
 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
mapcodeprevnextTop
 Title   : map
Usage : my $int = $relative->map();
$relative->map($int);
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.
elementcodeprevnextTop
 Title   : element
Usage : my $element = $relative->element();
$relative->element($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
positioncodeprevnextTop
 Title   : position
Usage : my $position = $relative->position();
$relative->position($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
descriptioncodeprevnextTop
 Title   : description
Usage : my $description = $relative->description();
$relative->description($description);
Function: Get/set a textual description of what this relative describes.
Returns : string
Args : none to get, OR
string to set
Methods code
newdescriptionprevnextTop
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 $self;
}
absolute_conversiondescriptionprevnextTop
sub absolute_conversion {
    my ($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;
}
typedescriptionprevnextTop
sub type {
    my $self = shift;
    return $self->{_use} || return;
}
mapdescriptionprevnextTop
sub map {
    my ($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}) ? $self->{_map} : return;
}
elementdescriptionprevnextTop
sub element {
    my ($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 $self->{_element} || return;
}
positiondescriptionprevnextTop
sub position {
    my ($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;
}
descriptiondescriptionprevnextTop
sub description {
    my $self = shift;
    if (@_) { $self->{desc} = shift }
    return $self->{desc} || '';
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. 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
of the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Sendu BalaTop
Email bix@sendu.me.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _