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.\" ========================================================================
.\"
.IX Title "Bio::Coordinate::Chain 3pm"
.TH Bio::Coordinate::Chain 3pm "2014-07-13" "perl v5.18.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\&  # create Bio::Coordinate::Pairs, or any MapperIs, somehow
\&  $pair1; $pair2;
\&
\&  # add them into a Chain
\&  $collection = Bio::Coordinate::Chain\->new;
\&  $collection\->add_mapper($pair1);
\&  $collection\->add_mapper($pair2);
\&
\&  # create a position and map it
\&  $pos = Bio::Location::Simple\->new (\-start => 5, \-end => 9 );
\&  $match = $collection\->map($pos);
\&  if ($match) {
\&      sprintf "Matches at %d\-%d\en", $match\->start, $match\->end,
\&  } else {
\&      print "No match\en";
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This class assumes that you have built several mappers and want to
link them together so that output from the previous mapper is the next
mappers input. This way you can build arbitrarily complex mappers from
simpler components.
.PP
Note that Chain does not do any sanity checking on its mappers. You
are solely responsible that input and output coordinate systems,
direction of mapping and parameters internal to mappers make sense
when chained together.
.PP
To put it bluntly, the present class is just a glorified foreach loop
over an array of mappers calling the map method.
.PP
It would be neat to an internal function that would generate a new
single step mapper from those included in the chain. It should speed
things up considerably. Any volunteers?
.SS "map"
.IX Subsection "map"
.Vb 6
\& Title   : map
\& Usage   : $newpos = $obj\->map($pos);
\& Function: Map the location through all the mappers in the chain.
\& Example :
\& Returns : new Location in the output coordiante system
\& Args    : a Bio::Location::Simple object
.Ve
.SS "Inherited methods"
.IX Subsection "Inherited methods"
.SS "add_mapper"
.IX Subsection "add_mapper"
.Vb 7
\& Title   : add_mapper
\& Usage   : $obj\->add_mapper($mapper)
\& Function: Pushes one Bio::Coodinate::MapperI into the list of mappers.
\&           Sets _is_sorted() to false.
\& Example :
\& Returns : 1 when succeeds, 0 for failure.
\& Args    : mapper object
.Ve
.SS "mappers"
.IX Subsection "mappers"
.Vb 6
\& Title   : mappers
\& Usage   : $obj\->mappers();
\& Function: Returns or sets a list of mappers.
\& Example :
\& Returns : array of mappers
\& Args    : array of mappers
.Ve
.SS "each_mapper"
.IX Subsection "each_mapper"
.Vb 6
\& Title   : each_mapper
\& Usage   : $obj\->each_mapper();
\& Function: Returns a list of mappers.
\& Example :
\& Returns : array of mappers
\& Args    : none
.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 "test"
.IX Subsection "test"
.Vb 7
\& Title   : test
\& Usage   : $obj\->test;
\& Function: test that both components of all pairs are of the same length.
\&           Ran automatically.
\& Example :
\& Returns : boolean
\& Args    :
.Ve
.SS "sort"
.IX Subsection "sort"
You do not really want to sort your chain, do you! This function does nothing
other than a warning.