Raw content of Bio::Tools::Prediction::Gene # $Id: Gene.pm,v 1.8 2002/10/22 07:38:48 lapp Exp $ # # BioPerl module for Bio::Tools::Prediction::Gene # # Cared for by Hilmar Lapp <hlapp@gmx.net> # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Prediction::Gene - a predicted gene structure feature =head1 SYNOPSIS See documentation of methods. =head1 DESCRIPTION A feature representing a predicted gene structure. This class actually inherits off Bio::SeqFeature::Gene::Transcript and therefore has all that functionality, plus a few methods supporting predicted sequence features, like a predicted CDS and a predicted translation. Exons held by an instance of this class will usually be instances of Bio::Tools::Prediction::Exon, although they do not have to be. Refer to the documentation of the class that produced the instance. Normally, you will not want to create an instance of this class yourself. Instead, classes representing the results of gene structure prediction programs will do that. =head1 FEEDBACK =head2 Mailing Lists 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 =head2 Reporting Bugs 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/ =head1 AUTHOR - Hilmar Lapp Email hlapp@gmx.net or hilmar.lapp@pharma.novartis.com Describe contact details here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Prediction::Gene; use vars qw(@ISA); use strict; use Bio::SeqFeature::Gene::Transcript; @ISA = qw(Bio::SeqFeature::Gene::Transcript); sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($primary) = $self->_rearrange([qw(PRIMARY)],@args); $primary = 'predicted_gene' unless $primary; $self->primary_tag($primary); return $self; } =head2 predicted_cds Title : predicted_cds Usage : $predicted_cds_dna = $gene->predicted_cds(); $gene->predicted_cds($predicted_cds_dna); Function: Get/Set the CDS (coding sequence) as predicted by a program. This method is independent of an attached_seq. There is no guarantee whatsoever that the returned CDS has anything to do (e.g., matches) with the sequence covered by the exons as annotated through this object. Example : Returns : A Bio::PrimarySeqI implementing object holding the DNA sequence defined as coding by a prediction of a program. Args : On set, a Bio::PrimarySeqI implementing object holding the DNA sequence defined as coding by a prediction of a program. =cut sub predicted_cds { my ($self, $cds) = @_; if(defined($cds)) { $self->{'_predicted_cds'} = $cds; } return $self->{'_predicted_cds'}; } =head2 predicted_protein Title : predicted_protein Usage : $predicted_protein_seq = $gene->predicted_protein(); $gene->predicted_protein($predicted_protein_seq); Function: Get/Set the protein translation as predicted by a program. This method is independent of an attached_seq. There is no guarantee whatsoever that the returned translation has anything to do with the sequence covered by the exons as annotated through this object, or the sequence returned by predicted_cds(), although it should usually be just the standard translation. Example : Returns : A Bio::PrimarySeqI implementing object holding the protein translation as predicted by a program. Args : On set, a Bio::PrimarySeqI implementing object holding the protein translation as predicted by a program. =cut sub predicted_protein { my ($self, $aa) = @_; if(defined($aa)) { $self->{'_predicted_aa'} = $aa; } return $self->{'_predicted_aa'}; } # # Everything else is just inherited from SeqFeature::GeneStructure. # 1;