mappers¶

 Title   : mappers
 Usage   : $obj->mappers();
 Function: Returns or sets a list of mappers.
 Example :
 Returns : array of mappers
 Args    : array of mappers

each_mapper¶

 Title   : each_mapper
 Usage   : $obj->each_mapper();
 Function: Returns a list of mappers.
 Example :
 Returns : list of mappers
 Args    : none

mapper_count¶

 Title   : mapper_count
 Usage   : my $count = $collection->mapper_count;
 Function: Get the count of the number of mappers stored
           in this collection
 Example :
 Returns : integer
 Args    : none

new¶

add_mapper¶

 Title   : add_mapper
 Usage   : $obj->add_mapper($mapper)
 Function: Pushes one Bio::Coordinate::MapperI into the list of mappers.
           Sets _is_sorted() to false.
 Example :
 Returns : 1 when succeeds, 0 for failure.
 Args    : mapper object

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 of all pairs are of the same length.
           Ran automatically.
 Example :
 Returns : boolean
 Args    :

map¶

 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 value in the output coordinate system
 Args    : integer

sort¶

 Title   : sort
 Usage   : $obj->sort;
 Function: Sort function so that all mappings are sorted by
           input coordinate start
 Example :
 Returns : 1
 Args    :

_map¶

 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

_is_sorted¶

 Title   : _is_sorted
 Usage   : $newpos = $obj->_is_sorted;
 Function: toggle for whether the (internal) coordinate mapper data are sorted
 Example :
 Returns : boolean
 Args    : boolean

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.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support¶

Please direct usage questions or support issues to the mailing list: bioperl-l@bioperl.org

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.

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:

  https://github.com/bioperl/%%7Bdist%7D