Bio::LiveSeq::Gene(3pm) 				User Contributed Perl Documentation				   Bio::LiveSeq::Gene(3pm)

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

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

perl v5.14.2							    2012-03-02						   Bio::LiveSeq::Gene(3pm)