Linux Certif

Toute la documentation sur la certification Linux LPI

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