Bio::SeqFeature::Gene TranscriptI
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Summary
Bio::SeqFeature::Gene::TranscriptI - Interface for a feature representing a
transcript of exons, promoter(s), UTR, and a poly-adenylation site.
Package variables
No package variables defined.
Included modules
Bio::SeqFeatureI
Carp
Inherit
Bio::SeqFeatureI
Synopsis
  #documentation needed
Description
A feature representing a transcript.
Methods
cdsDescriptionCode
exonsDescriptionCode
intronsDescriptionCode
mrnaDescriptionCode
parentDescriptionCode
poly_A_siteDescriptionCode
promotersDescriptionCode
proteinDescriptionCode
utrsDescriptionCode
Methods description
cdscode    nextTop
 Title   : cds()
 Usage   : $cds = $transcript->cds();
 Function: Get the CDS (coding sequence) of the transcript as a sequence
           object.

 Returns : A Bio::PrimarySeqI implementing object.
 Args    :
exonscodeprevnextTop
 Title   : exons()
 Usage   : @exons = $transcript->exons();
           @inital = $transcript->exons('Initial');
 Function: Get the individual exons this transcript comprises of, or all exons
           of a specified type.

           Refer to the documentation of the class that produced this 
           transcript 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
 Args    : An optional string specifying the type of the exon.
intronscodeprevnextTop
 Title   : introns()
 Usage   : @introns = $transcript->introns();
 Function: Get all introns this transcript comprises of.
 Returns : An array of Bio::SeqFeatureI implementing objects representing the
           introns.
 Args    :
mrnacodeprevnextTop
 Title   : mrna()
 Usage   : $mrna = $transcript->mrna();
 Function: Get the mRNA of the transcript as a sequence object.

 Returns : A Bio::PrimarySeqI implementing object.
 Args    :
parentcodeprevnextTop
 Title   : parent
 Usage   : $obj->parent($newval)
 Function: get the parent gene of the transcript
 Returns : value of parent - a Bio::SeqFeature::Gene::GeneStructureI-compliant object
 Args    : a Bio::SeqFeature::Gene::GeneStructureI-compliant object (optional)
poly_A_sitecodeprevnextTop
 Title   : poly_A_site()
 Usage   : $polyAsite = $transcript->poly_A_site();
 Function: Get the poly-adenylation site of this transcript.
 Returns : A Bio::SeqFeatureI implementing object.
 Args    :
promoterscodeprevnextTop
 Title   : promoters()
 Usage   : @proms = $transcript->promoters();
 Function: Get the promoter features of this transcript.

           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    :
proteincodeprevnextTop
 Title   : protein()
 Usage   : $protein = $transcript->protein();
 Function: Get the protein encoded by the transcript as a sequence object.

 Returns : A Bio::PrimarySeqI implementing object.
 Args    :
utrscodeprevnextTop
 Title   : utrs()
 Usage   : @utr_sites = $transcript->utrs();
 Function: Get the UTR regions this transcript comprises of.

           See Bio::SeqFeature::Gene::ExonI for properties of the
           returned objects.

 Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects
 Args    :
Methods code
cdsdescriptionprevnextTop
sub cds {
    my ($self) = @_;
    $self->throw_not_implemented();
}
exonsdescriptionprevnextTop
sub exons {
    my ($self, $type) = @_;
    $self->throw_not_implemented();
}
intronsdescriptionprevnextTop
sub introns {
    my ($self) = @_;
    $self->throw_not_implemented();
}
mrnadescriptionprevnextTop
sub mrna {
    my ($self) = @_;
    $self->throw_not_implemented();
}
parentdescriptionprevnextTop
sub parent {
   my ($self,$value) = @_;
   if( defined $value) {
       if ($value->isa("Bio::SeqFeature::Gene::GeneStructureI")) {
	   $self->{'parent'} = $value;
       } else {
	   $self->throw("$value must be a Bio::SeqFeature::Gene::GeneStructureI")
       }
    }
    return $self->{'parent'};
}


1;
}
poly_A_sitedescriptionprevnextTop
sub poly_A_site {
    my ($self) = @_;
    $self->throw_not_implemented();
}
promotersdescriptionprevnextTop
sub promoters {
    my ($self) = @_;
    $self->throw_not_implemented();
}
proteindescriptionprevnextTop
sub protein {
    my ($self) = @_;
    $self->throw_not_implemented();
}
utrsdescriptionprevnextTop
sub utrs {
    my ($self) = @_;
    $self->throw_not_implemented();
}
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://bio.perl.org/MailList.html             - About the mailing lists
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 email or the web:
  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/
AUTHOR - Hilmar LappTop
Email hlapp@gmx.net
Describe contact details here
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _