Bio::EnsEMBL UnconventionalTranscriptAssociation
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Summary
Bio::EnsEMBL::UnconventionalTranscriptAssociation - A class representing
an some sort of unconventional association between a gene and a
transcript.
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Utils::Argument qw ( rearrange )
Bio::EnsEMBL::Utils::Exception qw ( warning throw deprecate )
Synopsis
  $ex = new Bio::EnsEMBL::UnconventionalTranscriptAssociation( $gene,
    $transcript, $type );
Description
No description!
Methods
geneDescriptionCode
interaction_typeDescriptionCode
newDescriptionCode
transcriptDescriptionCode
Methods description
genecode    nextTop
  Args       : none
  Example    : $gene = $uta->gene()
  Description: Getter/setter for the gene part of this association.
  Returntype : Bio::EnsEMBL::Gene
  Exceptions : none
  Caller     : general
  Status     : At risk
interaction_typecodeprevnextTop
  Args       : none
  Example    : $type = $uta->interaction_type()
  Description: Getter/setter for the interaction_type of this association.
  Returntype : String
  Exceptions : none
  Caller     : General
  Status     : At risk
newcodeprevnextTop
  Args [1]   : Bio::EnsEMBL::Gene - the gene which is associated.
  Args [2]   : Bio::EnsEMBL::Transcript - the transcript which is associated.
  Args [3]   : String type - the type of assocation, e.g. "antisense",
               "sense_intronic","sense_overlaping_exonic","chimeric_sense_exonic".
  Example    : $uta = new Bio::EnsEMBL::UnconventionalTranscriptAssociation($gene, $transcript, "antisense")
  Description: create an UnconventionalTranscriptAssociation object.
  Returntype : Bio::EnsEMBL::UnconventionalTranscriptAssociation.
  Exceptions : Wrong argument types
  Caller     : general
  Status     : At risk
transcriptcodeprevnextTop
  Args       : none
  Example    : $transcript = $uta->transcript()
  Description: Getter/setter for the transcript part of this association.
  Returntype : Bio::EnsEMBL::Transcript
  Exceptions : none
  Caller     : General
  Status     : At risk
Methods code
genedescriptionprevnextTop
sub gene {
  my ($self) = shift;

  $self->{'gene'} = shift if (@_);
  return $self->{'gene'};
}
interaction_typedescriptionprevnextTop
sub interaction_type {
  my ($self) = shift;

  $self->{'interaction_type'} = shift if (@_);
  return $self->{'interaction_type'};

}

1;
}
newdescriptionprevnextTop
sub new {
  my ($class, $transcript, $gene, $type) = @_;

  $class = ref $class || $class;

  my $self = {};

  if( !ref $gene || ! $gene->isa("Bio::EnsEMBL::Gene") ) {
    throw("$gene is not a Bio::EnsEMBL::Gene!");
  }

  if( !ref $transcript || ! $transcript->isa("Bio::EnsEMBL::Transcript") ) {
    throw("$transcript is not a Bio::EnsEMBL::Transcript!");
  }

  $self->{'gene'} = $gene;
  $self->{'transcript'} = $transcript;
  $self->{'type'} = $type;

  return bless $self, $class;
}
transcriptdescriptionprevnextTop
sub transcript {
  my ($self) = shift;

  $self->{'transcript'} = shift if (@_);
  return $self->{'transcript'};
}
General documentation
LICENSETop
  Copyright (c) 1999-2009 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    /info/about/code_licence.html
CONTACTTop
  Please email comments or questions to the public Ensembl
  developers list at <ensembl-dev@ebi.ac.uk>.

  Questions may also be sent to the Ensembl help desk at
  <helpdesk@ensembl.org>.