Bio::EnsEMBL::Analysis::Tools::Pmatch ContigHit
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Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Utils::Argument qw ( rearrange )
Bio::EnsEMBL::Utils::Exception qw ( throw warning )
Inherit
Unavailable
Synopsis
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Description
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Methods
add_CoordPairDescriptionCode
each_ForwardPairDescriptionCode
each_ReversePairDescriptionCode
idDescriptionCode
newDescriptionCode
Methods description
add_CoordPaircode    nextTop
 Title   : add_CoordPair
 Usage   :
 Function: adds a CoordPair to the list making up this hit
 Example :
 Returns : 
 Args    :
each_ForwardPaircodeprevnextTop
 Title   : each_ForwardPair
 Usage   :
 Function: returns CoordPairs represeting hits between a prtein and the forward strand of the contig
 Example :
 Returns : 
 Args    :
each_ReversePaircodeprevnextTop
 Title   : each_Reverseair
 Usage   :
 Function: returns CoordPairs representing hits between a protein and the reverse strand of the contig
 Example :
 Returns : 
 Args    :
idcodeprevnextTop
 Title   : id
 Usage   :
 Function: get/set for contig id
 Example :
 Returns : 
 Args    :
newcodeprevnextTop
 Title   : new
 Usage   :
 Function: constructor
 Example :
 Returns : 
 Args    :
Methods code
add_CoordPairdescriptionprevnextTop
sub add_CoordPair {
  my ($self,$pair) = @_;
  throw('No coord pair') unless defined $pair;
  throw('$pair is not a Bio::EnsEMBL::Analysis::Tools::Pmatch::CoordPair') unless $pair->isa("Bio::EnsEMBL::Analysis::Tools::Pmatch::CoordPair");
  if($pair->strand == 1) {
    push(@{$self->{_forward_pairs}},$pair);
  }
  else {
    push(@{$self->{_reverse_pairs}},$pair);
  }
}
each_ForwardPairdescriptionprevnextTop
sub each_ForwardPair {
  my ($self) = @_;
  return $self->{_forward_pairs};
}
each_ReversePairdescriptionprevnextTop
sub each_ReversePair {
  my ($self) = @_;
  return $self->{_reverse_pairs};
}
1;
}
iddescriptionprevnextTop
sub id {
  my ($self,$id) = @_;
  if ($id) {
    $self->{'id'} = $id;
  }
  return $self->{'id'};
}
newdescriptionprevnextTop
sub new {
  my ($class, @args) = @_;
  my $self = bless {}, $class;

  my ($id) = rearrange(['ID'], @args);

  throw("No id") unless defined $id;
  $self->id($id);
 
  $self->{'_forward_pairs'} = [];
  $self->{'_reverse_pairs'} = [];

  return $self;
}
General documentation
No general documentation available.