Bio::Coordinate Pair
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Summary
Bio::Coordinate::Pair - Continuous match between two coordinate sets
Package variables
No package variables defined.
Included modules
Bio::Coordinate::Result
Bio::Coordinate::Result::Gap
Bio::Coordinate::Result::Match
Inherit
Bio::Coordinate::MapperI Bio::Root::Root
Synopsis
  use Bio::Location::Simple;
use Bio::Coordinate::Pair;
my $match1 = Bio::Location::Simple->new (-seq_id => 'propeptide', -start => 21, -end => 40, -strand=>1 ); my $match2 = Bio::Location::Simple->new (-seq_id => 'peptide', -start => 1, -end => 20, -strand=>1 ); my $pair = Bio::Coordinate::Pair->new(-in => $match1, -out => $match2 ); # location to match $pos = Bio::Location::Simple->new (-start => 25, -end => 25, -strand=> -1 ); # results are in a Bio::Coordinate::Result # they can be Matches and Gaps; are Bio::LocationIs $res = $pair->map($pos); $res->isa('Bio::Coordinate::Result'); $res->each_match == 1; $res->each_gap == 0; $res->each_Location == 1; $res->match->start == 5; $res->match->end == 5; $res->match->strand == -1; $res->match->seq_id eq 'peptide';
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.
The map() method returns Bio::Coordinate::Results with
Bio::Coordinate::Result::Gaps. The calling code have to deal (process
or ignore) them.
Methods
new
No description
Code
inDescriptionCode
outDescriptionCode
swapDescriptionCode
strandDescriptionCode
testDescriptionCode
mapDescriptionCode
_mapDescriptionCode
Methods description
incode    nextTop
 Title   : in
Usage : $obj->in('peptide');
Function: Set and read the input coordinate system.
Example :
Returns : value of input system
Args : new value (optional), Bio::LocationI
outcodeprevnextTop
 Title   : out
Usage : $obj->out('peptide');
Function: Set and read the output coordinate system.
Example :
Returns : value of output system
Args : new value (optional), Bio::LocationI
swapcodeprevnextTop
 Title   : swap
Usage : $obj->swap;
Function: Swap the direction of mapping; input <-> output
Example :
Returns : 1
Args :
strandcodeprevnextTop
 Title   : strand
Usage : $obj->strand;
Function: Get strand value for the pair
Example :
Returns : ( 1 | 0 | -1 )
Args :
testcodeprevnextTop
 Title   : test
Usage : $obj->test;
Function: test that both components are of the same length
Example :
Returns : ( 1 | undef )
Args :
mapcodeprevnextTop
 Title   : map
Usage : $newpos = $obj->map($pos);
Function: Map the location from the input coordinate system
to a new value in the output coordinate system.
Example :
Returns : new Bio::LocationI in the output coordinate system or undef
Args : Bio::LocationI object
_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($in, $out) =
	$self->_rearrange([qw(IN
                              OUT
			     )],
			 @args);

    $in  && $self->in($in);
    $out  && $self->out($out);
    return $self; # success - we hope!
}
indescriptionprevnextTop
sub in {
   my ($self,$value) = @_;
   if( defined $value) {
       $self->throw("Not a valid input Bio::Location [$value] ")
	   unless $value->isa('Bio::LocationI');
       $self->{'_in'} = $value;
   }
   return $self->{'_in'};
}
outdescriptionprevnextTop
sub out {
   my ($self,$value) = @_;
   if( defined $value) {
       $self->throw("Not a valid output coordinate Bio::Location [$value] ")
	   unless $value->isa('Bio::LocationI');
       $self->{'_out'} = $value;
   }
   return $self->{'_out'};
}
swapdescriptionprevnextTop
sub swap {
   my ($self) = @_;
   ($self->{'_in'}, $self->{'_out'}) = ($self->{'_out'}, $self->{'_in'});
   return 1;
}
stranddescriptionprevnextTop
sub strand {
   my ($self) = @_;
   $self->warn("Outgoing coordinates are not defined")
       unless $self->out;
   $self->warn("Incoming coordinates are not defined")
       unless $self->in;

   return ($self->in->strand || 0) * ($self->out->strand || 0);
}
testdescriptionprevnextTop
sub test {
   my ($self) = @_;
   $self->warn("Outgoing coordinates are not defined")
       unless $self->out;
   $self->warn("Incoming coordinates are not defined")
       unless $self->in;
   return ($self->in->end - $self->in->start) == ($self->out->end - $self->out->start);
}
mapdescriptionprevnextTop
sub map {
   my ($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;


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

       my $result = Bio::Coordinate::Result->new();
       foreach my $loc ( $value->sub_Location(1) ) {
           my $res = $self->_map($loc);
           map { $result->add_sub_Location($_) } $res->each_Location;
       }
       return $result;
   } else {
       return $self->_map($value);
   }
}
_mapdescriptionprevnextTop
sub _map {
   my ($self,$value) = @_;

   my $result = Bio::Coordinate::Result->new();

   my $offset = $self->in->start - $self->out->start;
   my $start  = $value->start - $offset;
   my $end    = $value->end - $offset;
   
   my $match = Bio::Location::Simple->new;
   $match->location_type($value->location_type);
   $match->strand($self->strand);

   #within
# |-------------------------|
# |-|
if ($start >= $self->out->start and $end <= $self->out->end) { $match->seq_id($self->out->seq_id); $result->seq_id($self->out->seq_id); if ($self->strand >= 0) { $match->start($start); $match->end($end); } else { $match->start($self->out->end - $end + $self->out->start); $match->end($self->out->end - $start + $self->out->start); } if ($value->strand) { $match->strand($match->strand * $value->strand); $result->strand($match->strand); } bless $match, 'Bio::Coordinate::Result::Match'; $result->add_sub_Location($match); } #out
# |-------------------------|
# |-| or |-|
elsif ( ($end < $self->out->start or $start > $self->out->end ) or #insertions just outside the range need special settings
($value->location_type eq 'IN-BETWEEN' and ($end = $self->out->start or $start = $self->out->end))) { $match->seq_id($self->in->seq_id); $result->seq_id($self->in->seq_id); $match->start($value->start); $match->end($value->end); $match->strand($value->strand); bless $match, 'Bio::Coordinate::Result::Gap'; $result->add_sub_Location($match); } #partial I
# |-------------------------|
# |-----|
elsif ($start < $self->out->start and $end <= $self->out->end ) { $result->seq_id($self->out->seq_id); if ($value->strand) { $match->strand($match->strand * $value->strand); $result->strand($match->strand); } my $gap = Bio::Location::Simple->new; $gap->start($value->start); $gap->end($self->in->start - 1); $gap->strand($value->strand); $gap->seq_id($self->in->seq_id); bless $gap, 'Bio::Coordinate::Result::Gap'; $result->add_sub_Location($gap); # match
$match->seq_id($self->out->seq_id); if ($self->strand >= 0) { $match->start($self->out->start); $match->end($end); } else { $match->start($self->out->end - $end + $self->out->start); $match->end($self->out->end); } bless $match, 'Bio::Coordinate::Result::Match'; $result->add_sub_Location($match); } #partial II
# |-------------------------|
# |------|
elsif ($start >= $self->out->start and $end > $self->out->end ) { $match->seq_id($self->out->seq_id); $result->seq_id($self->out->seq_id); if ($value->strand) { $match->strand($match->strand * $value->strand); $result->strand($match->strand); } if ($self->strand >= 0) { $match->start($start); $match->end($self->out->end); } else { $match->start($self->out->start); $match->end($self->out->end - $start + $self->out->start); } bless $match, 'Bio::Coordinate::Result::Match'; $result->add_sub_Location($match); my $gap = Bio::Location::Simple->new; $gap->start($self->in->end + 1); $gap->end($value->end); $gap->strand($value->strand); $gap->seq_id($self->in->seq_id); bless $gap, 'Bio::Coordinate::Result::Gap'; $result->add_sub_Location($gap); } #enveloping
# |-------------------------|
# |---------------------------------|
elsif ($start < $self->out->start and $end > $self->out->end ) { $result->seq_id($self->out->seq_id); if ($value->strand) { $match->strand($match->strand * $value->strand); $result->strand($match->strand); } # gap1
my $gap1 = Bio::Location::Simple->new; $gap1->start($value->start); $gap1->end($self->in->start - 1); $gap1->strand($value->strand); $gap1->seq_id($self->in->seq_id); bless $gap1, 'Bio::Coordinate::Result::Gap'; $result->add_sub_Location($gap1); # match
$match->seq_id($self->out->seq_id); $match->start($self->out->start); $match->end($self->out->end); bless $match, 'Bio::Coordinate::Result::Match'; $result->add_sub_Location($match); # gap2
my $gap2 = Bio::Location::Simple->new; $gap2->start($self->in->end + 1); $gap2->end($value->end); $gap2->strand($value->strand); $gap2->seq_id($self->in->seq_id); bless $gap2, 'Bio::Coordinate::Result::Gap'; $result->add_sub_Location($gap2); } else { $self->throw("Should not be here!"); } return $result; } 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 _