Bio::Map RelativeI
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Summary
Bio::Map::RelativeI - Interface for describing what a Position's coordiantes are
relative to.
Package variables
No package variables defined.
Inherit
Bio::Root::RootI
Synopsis
    # do not use this module directly
# See Bio::Map::Relative for an example of
# implementation.
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
absolute_conversionDescriptionCode
typeDescriptionCode
mapDescriptionCode
elementDescriptionCode
positionDescriptionCode
descriptionDescriptionCode
Methods description
absolute_conversioncode    nextTop
 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 got 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 got 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
absolute_conversiondescriptionprevnextTop
sub absolute_conversion {
    my $self = shift;
    $self->throw_not_implemented();
}
typedescriptionprevnextTop
sub type {
    my $self = shift;
    $self->throw_not_implemented();
}
mapdescriptionprevnextTop
sub map {
    my $self = shift;
    $self->throw_not_implemented();
}
elementdescriptionprevnextTop
sub element {
    my $self = shift;
    $self->throw_not_implemented();
}
positiondescriptionprevnextTop
sub position {
    my $self = shift;
    $self->throw_not_implemented();
}
descriptiondescriptionprevnextTop
sub description {
    my $self = shift;
    $self->throw_not_implemented();
}

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 _