Bio::Coordinate MapperI
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Coordinate::MapperI - Interface describing coordinate mappers
Package variables
No package variables defined.
Inherit
Bio::Root::RootI
Synopsis
  # not to be used directly
Description
MapperI defines methods for classes capable for mapping locations
between coordinate systems.
Methods
inDescriptionCode
outDescriptionCode
swapDescriptionCode
testDescriptionCode
mapDescriptionCode
return_matchDescriptionCode
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    :
testcodeprevnextTop
 Title   : test
 Usage   : $obj->test;
 Function: test that both components are of same length
 Example :
 Returns : ( 1 | undef )
 Args    :
mapcodeprevnextTop
 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_matchcodeprevnextTop
 Title   : return_match
 Usage   : $obj->return_match(1);
 Function: A flag to turn on the simplified mode of
           returning only one joined Match object or undef
 Example :
 Returns : boolean
 Args    : boolean (optional)
Methods code
indescriptionprevnextTop
sub in {
   my ($self,$value) = @_;

   $self->throw_not_implemented();
}
outdescriptionprevnextTop
sub out {
   my ($self,$value) = @_;

   $self->throw_not_implemented();
}
swapdescriptionprevnextTop
sub swap {
   my ($self) = @_;

   $self->throw_not_implemented();
}
testdescriptionprevnextTop
sub test {
   my ($self) = @_;

   $self->throw_not_implemented();
}
mapdescriptionprevnextTop
sub map {
   my ($self,$value) = @_;

   $self->throw_not_implemented();
}
return_matchdescriptionprevnextTop
sub return_match {
   my ($self,$value) = @_;
   if( defined $value) {
       $value ? ( $self->{'_return_match'} = 1 ) :
                ( $self->{'_return_match'} = 0 );
   }
   return $self->{'_return_match'} || 0 ;
}
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
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:
  http://bugzilla.open-bio.org/
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 _