Provided by: libbio-perl-perl_1.6.901-2_all bug


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


         # documentation needed


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

AUTHOR - Joseph A.L. Insana



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

         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
                   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

        Title   : verbose
        Usage   : $self->verbose(0)
        Function: Sets verbose level for how ->warn behaves
                  -1 = silent: no warning
                   0 = reduced: minimal warnings
                   1 = default: all warnings
                   2 = extended: all warnings + stack trace dump
                   3 = paranoid: a warning becomes a throw and the program dies

                  Note: a quick way to set all LiveSeq objects at the same verbosity
                  level is to change the DNA level object, since they all look to
                  that one if their verbosity_level attribute is not set.
                  But the method offers fine tuning possibility by changing the
                  verbose level of each object in a different way.

                  So for example, after $loader= and $gene= have been retrieved
                  by a program, the command $gene->verbose(0); would
                  set the default verbosity level to 0 for all objects.

        Returns : the current verbosity level
        Args    : -1,0,1,2 or 3