Bio::LiveSeq::Gene - Range abstract class for LiveSeq
# documentation needed
This is used as storage for all object references concerning a particular gene.
Email: Insana@ebi.ac.uk, email@example.com
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
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