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.\" ========================================================================
.\"
.IX Title "Bio::Coordinate::Pair 3pm"
.TH Bio::Coordinate::Pair 3pm "2014-07-13" "perl v5.18.2" "User Contributed Perl Documentation"
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.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\&  use Bio::Location::Simple;
\&  use Bio::Coordinate::Pair;
\&
\&  my $match1 = Bio::Location::Simple\->new
\&      (\-seq_id => \*(Aqpropeptide\*(Aq, \-start => 21, \-end => 40, \-strand=>1 );
\&  my $match2 = Bio::Location::Simple\->new
\&      (\-seq_id => \*(Aqpeptide\*(Aq, \-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(\*(AqBio::Coordinate::Result\*(Aq);
\&  $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 \*(Aqpeptide\*(Aq;
.Ve
.SH "DESCRIPTION"
.IX Header "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.
.PP
The \fImap()\fR method returns Bio::Coordinate::Results with
Bio::Coordinate::Result::Gaps. The calling code have to deal (process
or ignore) them.
.SS "new"
.IX Subsection "new"
.SS "in"
.IX Subsection "in"
.Vb 6
\& Title   : in
\& Usage   : $obj\->in(\*(Aqpeptide\*(Aq);
\& Function: Set and read the input coordinate system.
\& Example :
\& Returns : value of input system
\& Args    : new value (optional), Bio::LocationI
.Ve
.SS "out"
.IX Subsection "out"
.Vb 6
\& Title   : out
\& Usage   : $obj\->out(\*(Aqpeptide\*(Aq);
\& Function: Set and read the output coordinate system.
\& Example :
\& Returns : value of output system
\& Args    : new value (optional), Bio::LocationI
.Ve
.SS "swap"
.IX Subsection "swap"
.Vb 6
\& Title   : swap
\& Usage   : $obj\->swap;
\& Function: Swap the direction of mapping; input <\-> output
\& Example :
\& Returns : 1
\& Args    :
.Ve
.SS "strand"
.IX Subsection "strand"
.Vb 6
\& Title   : strand
\& Usage   : $obj\->strand;
\& Function: Get strand value for the pair
\& Example :
\& Returns : ( 1 | 0 | \-1 )
\& Args    :
.Ve
.SS "test"
.IX Subsection "test"
.Vb 6
\& Title   : test
\& Usage   : $obj\->test;
\& Function: test that both components are of the same length
\& Example :
\& Returns : ( 1 | undef )
\& Args    :
.Ve
.SS "map"
.IX Subsection "map"
.Vb 7
\& 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
.Ve
.SS "_map"
.IX Subsection "_map"
.Vb 8
\& 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
.Ve