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

verbose

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