Bio::SeqFeature::Gene GeneStructureI
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::SeqFeature::Gene::GeneStructureI - A feature representing an arbitrarily
complex structure of a gene
Package variables
No package variables defined.
Included modules
Carp
Inherit
Bio::SeqFeatureI
Synopsis
  #documentation needed
Description
A feature representing a gene structure.
Methods
transcriptsDescriptionCode
promotersDescriptionCode
exonsDescriptionCode
intronsDescriptionCode
poly_A_sitesDescriptionCode
utrsDescriptionCode
Methods description
transcriptscode    nextTop
 Title   : transcripts()
Usage : @transcripts = $gene->transcripts();
Function: Get the transcript features/sites of this gene structure.
See Bio::SeqFeature::Gene::TranscriptI for properties of the returned objects. Returns : An array of Bio::SeqFeature::Gene::TranscriptI implementing objects representing the promoter regions or sites. Args :
promoterscodeprevnextTop
 Title   : promoters()
Usage : @prom_sites = $gene->promoters();
Function: Get the promoter features/sites of this gene structure.
Note that OO-modeling of regulatory elements is not stable yet. This means that this method might change or even disappear in a future release. Be aware of this if you use it. Returns : An array of Bio::SeqFeatureI implementing objects representing the promoter regions or sites. Args :
exonscodeprevnextTop
 Title   : exons()
Usage : @exons = $gene->exons();
@inital = $gene->exons('Initial');
Function: Get all exon features or all exons of specified type of this gene
structure.
Refer to the documentation of the class that produced this gene structure object for information about the possible types. See Bio::SeqFeature::Gene::ExonI for properties of the returned objects. Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects representing the exon regions. Args : An optional string specifying the type of the exon.
intronscodeprevnextTop
 Title   : introns()
Usage : @introns = $gene->introns();
Function: Get all introns of this gene structure.
Returns : An array of Bio::SeqFeatureI implementing objects representing the
introns.
Args :
poly_A_sitescodeprevnextTop
 Title   : poly_A_sites()
Usage : @polyAsites = $gene->poly_A_sites();
Function: Get the poly-adenylation features/sites of this gene structure.
Returns : An array of Bio::SeqFeatureI implementing objects representing the
poly-adenylation regions or sites.
Args :
utrscodeprevnextTop
 Title   : utrs()
Usage : @utr_sites = $gene->utrs();
Function: Get the UTR features/sites of this gene structure.
See Bio::SeqFeature::Gene::ExonI for properties of the returned objects. Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects representing the UTR regions or sites. Args :
Methods code
transcriptsdescriptionprevnextTop
sub transcripts {
    my ($self) = @_;
    $self->throw_not_implemented();
}
promotersdescriptionprevnextTop
sub promoters {
    my ($self) = @_;
    $self->throw_not_implemented();
}
exonsdescriptionprevnextTop
sub exons {
    my ($self, $type) = @_;
    $self->throw_not_implemented();
}
intronsdescriptionprevnextTop
sub introns {
    my ($self) = @_;
    $self->throw_not_implemented();
}
poly_A_sitesdescriptionprevnextTop
sub poly_A_sites {
    my ($self) = @_;
    $self->throw_not_implemented();
}
utrsdescriptionprevnextTop
sub utrs {
    my ($self) = @_;
    $self->throw_not_implemented();
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this
and other Bioperl modules. Send your comments and suggestions preferably
to one of the Bioperl mailing lists. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Hilmar LappTop
Email hlapp@gmx.net
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _