Christopher Fields > BioPerl > Bio::Coordinate::MapperI

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Module Version: 1.006924   Source  

SYNOPSIS ^

  # not to be used directly

DESCRIPTION ^

MapperI defines methods for classes capable for mapping locations between coordinate systems.

in

 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

out

 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

swap

 Title   : swap
 Usage   : $obj->swap;
 Function: Swap the direction of mapping: input <-> output)
 Example :
 Returns : 1
 Args    :

test

 Title   : test
 Usage   : $obj->test;
 Function: test that both components are of same length
 Example :
 Returns : ( 1 | undef )
 Args    :

map

 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.
 Example :
 Returns : new value in the output coordiante system
 Args    : Bio::LocationI

return_match

 Title   : return_match
 Usage   : $obj->return_match(1);
 Function: A flag to turn on the simplified mode of
           returning only one joined Match object or undef
 Example :
 Returns : boolean
 Args    : boolean (optional)
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