nozero¶

 Title   : nozero
 Usage   : $obj->nozero(1);
 Function: Flag to disable the use of zero in the input,
           output or both coordinate systems. Use of coordinate
           systems without zero is a peculiarity  common in
           human genetics community.
 Example :
 Returns : 0 (default), or 'in', 'out', 'in&out'
 Args    : 0 (default), or 'in', 'out', 'in&out'

new¶

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)

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)

strict¶

 Title   : strict
 Usage   : $obj->strict('peptide');
 Function: Set and read whether strict boundaried of coordinate
           systems are enforced.
           When strict is on, the end of the coordinate range must be defined.
 Example :
 Returns : boolean
 Args    : boolean (optional)

graph¶

 Title   : graph
 Usage   : $obj->graph($new_graph);
 Function: Set and read the graph object representing relationships
           between coordinate systems
 Example :
 Returns : Bio::Coordinate::Graph object
 Args    : new Bio::Coordinate::Graph object (optional)

peptide¶

 Title   : peptide
 Usage   : $obj->peptide_offset($peptide_coord);
 Function: Read and write the offset of peptide from the start of propeptide
           and peptide length
 Returns : a Bio::Location::Simple object
 Args    : a Bio::LocationI object

peptide_offset¶

 Title   : peptide_offset
 Usage   : $obj->peptide_offset(20);
 Function: Set and read the offset of peptide from the start of propeptide
 Returns : set value or 0
 Args    : new value (optional)

peptide_length¶

 Title   : peptide_length
 Usage   : $obj->peptide_length(20);
 Function: Set and read the offset of peptide from the start of propeptide
 Returns : set value or 0
 Args    : new value (optional)

exons¶

 Title   : exons
 Usage   : $obj->exons(@exons);
 Function: Set and read the offset of CDS from the start of transcript
           You do not have to sort the exons before calling this method as
           they will be sorted automatically.
           If you have not defined the CDS, is will be set to span all
           exons here.
 Returns : array of Bio::LocationI exons in genome coordinates or 0
 Args    : array of Bio::LocationI exons in genome (or entry) coordinates

cds¶

 Title   : cds
 Usage   : $obj->cds(20);
 Function: Set and read the offset of CDS from the start of transcipt
           Simple input can be an integer which gives the start of the
           coding region in genomic coordinate. If you want to provide
           the end of the coding region or indicate the use of the
           opposite strand, you have to pass a Bio::RangeI
           (e.g. Bio::Location::Simple or Bio::SegFeature::Generic)
           object to this method.
 Returns : set value or 0
 Args    : new value (optional)

map¶

 Title   : map
 Usage   : $newpos = $obj->map(5);
 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    : a Bio::Location::Simple

direction¶

 Title   : direction
 Usage   : $obj->direction('peptide');
 Function: Read-only method for the direction of mapping deduced from
           predefined input and output coordinate names.
 Example :
 Returns : 1 or -1, mapping direction
 Args    : new value (optional)

swap¶

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

to_string¶

 Title   : to_string
 Usage   : $newpos = $obj->to_string(5);
 Function: Dump the internal mapper values into a human readable format
 Example :
 Returns : string
 Args    :

_clone_loc¶

 Title   : _clone_loc
 Usage   : $copy_of_loc = $obj->_clone_loc($loc);
 Function: Make a deep copy of a simple location
 Returns : a Bio::Location::Simple object
 Args    : a Bio::Location::Simple object to be cloned

_mapper_code2string¶

_mapper_string2code¶

_create_pair¶

 Title   : _create_pair
 Usage   : $mapper = $obj->_create_pair('chr', 'gene', 0, 2555, 10000, -1);
 Function: Internal helper method to create a mapper between
           two coordinate systems
 Returns : a Bio::Coordinate::Pair object
 Args    : string, input coordinate system name,
           string, output coordinate system name,
           boolean, strict mapping
           positive integer, offset
           positive integer, length
           1 || -1 , strand

_translate¶

 Title   : _translate
 Usage   : $newpos = $obj->_translate($loc);
 Function: Translate the location from the CDS coordinate system
           to a new value in the propeptide coordinate system.
 Example :
 Returns : new location
 Args    : a Bio::Location::Simple or Bio::Location::SplitLocationI

_frame¶

_reverse_translate¶

 Title   : _reverse_translate
 Usage   : $newpos = $obj->_reverse_translate(5);
 Function: Reverse translate the location from the propeptide
           coordinate system to a new value in the CSD.
           Note that a single peptide location expands to cover
           the codon triplet
 Example :
 Returns : new location in the CDS coordinate system
 Args    : a Bio::Location::Simple or Bio::Location::SplitLocationI

_check_direction¶

 Title   : _check_direction
 Usage   : $obj->_check_direction();
 Function: Check and swap when needed the direction the location
           mapping Pairs based on input and output values
 Example :
 Returns : new location
 Args    : a Bio::Location::Simple

_get_path¶

 Title   : _get_path
 Usage   : $obj->_get_path('peptide');
 Function: internal method for finding that shortest path between
           input and output coordinate systems.
           Calculations and caching are handled by the graph class.
           See L<Bio::Coordinate::Graph>.
 Example :
 Returns : array of the mappers
 Args    : none

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