NAME

Bio::LiveSeq::Gene - Range abstract class for LiveSeq

SYNOPSIS

  # documentation needed

DESCRIPTION

This is used as storage for all object references concerning a particular gene.

AUTHOR - Joseph A.L. Insana

Email: Insana@ebi.ac.uk, jinsana@gmx.net

Address:

     EMBL Outstation, European Bioinformatics Institute
     Wellcome Trust Genome Campus, Hinxton
     Cambs. CB10 1SD, United Kingdom 

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

  Title   : new
  Usage   : $gene = Bio::LiveSeq::Gene->new(-name => "name",
                                            -features => $hashref
                                            -upbound => $min
                                            -downbound => $max);

  Function: generates a new Bio::LiveSeq::Gene
  Returns : reference to a new object of class Gene
  Errorcode -1
  Args    : one string and one hashreference containing all features defined
            for the Gene and the references to the LiveSeq objects for those
            features.
            Two labels for defining boundaries of the gene. Usually the
            boundaries will reflect max span of transcript, exon... features,
            while the DNA sequence will be created with some flanking regions
            (e.g. with the EMBL_SRS::gene2liveseq routine).
            If these two labels are not given, they will default to the start
            and end of the DNA object.
  Note    : the format of the hash has to be like
               DNA => reference to LiveSeq::DNA object
               Transcripts => reference to array of transcripts objrefs
               Transclations => reference to array of transcripts objrefs
               Exons => ....
               Introns => ....
               Prim_Transcripts => ....
               Repeat_Units => ....
               Repeat_Regions => ....
            Only DNA and Transcripts are mandatory