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.\" ========================================================================
.\"
.IX Title "Bio::Coordinate::Pair 3pm"
.TH Bio::Coordinate::Pair 3pm "2020-11-24" "perl v5.32.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.SH "NAME"
Bio::Coordinate::Pair \- Continuous match between two coordinate sets.
.SH "VERSION"
.IX Header "VERSION"
version 1.007001
.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 \fBmap()\fR method returns Bio::Coordinate::Results with
Bio::Coordinate::Result::Gaps. The calling code have to deal (process
or ignore) them.
.SH "METHODS"
.IX Header "METHODS"
.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
.SH "INTERNAL METHODS"
.IX Header "INTERNAL METHODS"
.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
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing lists"
.IX Subsection "Mailing lists"
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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting bugs"
.IX Subsection "Reporting bugs"
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:
.PP
.Vb 1
\&  https://github.com/bioperl/%%7Bdist%7D
.Ve
.SH "AUTHOR"
.IX Header "AUTHOR"
Heikki Lehvaslaiho <heikki@bioperl.org>
.SH "COPYRIGHT"
.IX Header "COPYRIGHT"
This software is copyright (c) by Heikki Lehvaslaiho.
.PP
This software is available under the same terms as the perl 5 programming language system itself.