Bio::Coordinate ExtrapolatingPair
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Summary
Bio::Coordinate::ExtrapolatingPair - Continuous match between two coordinate sets
Package variables
No package variables defined.
Included modules
Bio::LocationI
Bio::Root::Root
Inherit
Bio::Coordinate::Pair
Synopsis
  use Bio::Location::Simple;
use Bio::Coordinate::ExtrapolatingPair;
$match1 = Bio::Location::Simple->new (-seq_id => 'propeptide', -start => 21, -end => 40, -strand=>1 ); $match2 = Bio::Location::Simple->new (-seq_id => 'peptide', -start => 1, -end => 20, -strand=>1 ); $pair = Bio::Coordinate::ExtrapolatingPair-> new(-in => $match1, -out => $match2, -strict => 1 ); $pos = Bio::Location::Simple->new (-start => 40, -end => 60, -strand=> 1 ); $res = $pair->map($pos); $res->start eq 20; $res->end eq 20;
Description
This class represents a one continuous match between two coordinate
systems represented by Bio::Location::Simple objects. The relationship
is directed and reversible. It implements methods to ensure internal
consistency, and map continuous and split locations from one
coordinate system to another.
This class is an elaboration of Bio::Coordinate::Pair. The map
function returns only matches which is the mode needed most of
tehtime. By default the matching regions between coordinate systems
are boundless, so that you can say e.g. that gene starts from here in
the chromosomal coordinate system and extends indefinetely in both
directions. If you want to define the matching regions exactly, you
can do that and set strict() to true.
Methods
new
No description
Code
strictDescriptionCode
mapDescriptionCode
_mapDescriptionCode
Methods description
strictcode    nextTop
 Title   : strict
Usage : $obj->strict(1);
Function: Set and read the strictness of the coordinate system.
Example :
Returns : value of input system
Args : boolean
mapcodeprevnextTop
 Title   : map
Usage : $newpos = $obj->map($loc);
Function: Map the location from the input coordinate system
to a new value in the output coordinate system.
In extrapolating coodinate system there is no location zero. Locations are... Example : Returns : new location in the output coordinate system or undef Args : Bio::Location::Simple
_mapcodeprevnextTop
 Title   : _map
Usage : $newpos = $obj->_map($simpleloc);
Function: Internal method that does the actual mapping. Called
multiple times by map() if the location to be mapped is a
split location
Example : Returns : new location in the output coordinate system or undef Args : Bio::Location::Simple
Methods code
newdescriptionprevnextTop
sub new {
    my($class,@args) = @_;
    my $self = $class->SUPER::new(@args);

    my($strict) =
	$self->_rearrange([qw(STRICT
			     )],
			 @args);

    $strict  && $self->strict($strict);
    return $self;
}
strictdescriptionprevnextTop
sub strict {
   my ($self,$value) = @_;
   if( defined $value) {
       $self->{'_strict'} = 1 if $value;
   }
   return $self->{'_strict'};
}
mapdescriptionprevnextTop
sub map {
   my ($self,$value) = @_;

   $self->throw("Need to pass me a value.")
       unless defined $value;
   $self->throw("I need a Bio::Location, not [$value]")
       unless $value->isa('Bio::LocationI');
   $self->throw("Input coordinate system not set")
       unless $self->in;
   $self->throw("Output coordinate system not set")
       unless $self->out;

   my $match;

   if ($value->isa("Bio::Location::SplitLocationI")) {

       my $split = Bio::Coordinate::Result->new(-seq_id=>$self->out->seq_id);
       foreach my $loc ( sort { $a->start <=> $b->start }
                         $value->sub_Location ) {

           $match = $self->_map($loc);
           $split->add_sub_Location($match) if $match;

       }
       $split->each_Location ? (return $split) : return ;

   } else {
       return $self->_map($value);
   }
}
_mapdescriptionprevnextTop
sub _map {
   my ($self,$value) = @_;

   my ($offset, $start, $end);

   if ($self->strand == -1) {
       $offset = $self->in->end + $self->out->start;
       $start = $offset - $value->end;
       $end = $offset - $value->start ;
   } else { # undef, 0 or 1
$offset = $self->in->start - $self->out->start; $start = $value->start - $offset; $end = $value->end - $offset; } # strict prevents matches outside stated range
if ($self->strict) { return if $start < 0 and $end < 0; return if $start > $self->out->end; $start = 1 if $start < 0; $end = $self->out->end if $end > $self->out->end; } my $match = Bio::Location::Simple-> new(-start => $start, -end => $end, -strand => $self->strand, -seq_id => $self->out->seq_id, -location_type => $value->location_type ); $match->strand($match->strand * $value->strand) if $value->strand; bless $match, 'Bio::Coordinate::Result::Match'; return $match; } 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 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 - Heikki LehvaslaihoTop
Email: heikki-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _