METHODS

new

  Arg [gff_file]    : String - GFF file to perform annotation with
  Arg [est_file]    : String (Optional) - GFF file with EST to find annotation if none
                      have been found in the 

  Example     : my $annotation = CracTools::GFF::Annotation->new(gff_file => $gff);
  Description : Create a new CracTools::ChimCT::Analyzer::Annotation object
  ReturnType  : CracTools::ChimCT::Analyzer::Annotation
  Exceptions  : none

getCandidateCodingPriority

  Arg [1] : String - pos_start
  Arg [2] : String - pos_end
  Arg [3] : hash - candidate

  Description : Method used to give a priority to a candidate in CracTools;:Annotator
                The best priority is 0. A priority of -1 means that this candidate
                should be avoided.
  ReturnType  : ($priority,$type)

getCandidateNonCodingPriority

  Arg [1] : String - pos_start
  Arg [2] : String - pos_end
  Arg [3] : hash - candidate

  Description : Method used to give a priority to a candidate in CracTools;:Annotator
                The best priority is 0. A priority of -1 means that this candidate
                should be avoided.
  ReturnType  : ($priority,$type)