Christopher Fields > BioPerl-1.6.921 > Bio::LiveSeq::Gene

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Module Version: 1.006921   Source   Latest Release: BioPerl-1.6.924

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
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