Bio::EnsEMBL::Pipeline Alignment
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Summary
  
Bio::EnsEMBL::Pipeline::Alignment.pm
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Utils::Argument qw ( rearrange )
Inherit
Unavailable
Synopsis
Description
A very basic object that contains sequences of an alignment
(as AlignmentSeq objects). Stores (or at least will store)
information about the alignment too.
Methods
add_sequence
No description
Code
alignment_name
No description
Code
fetch_AlignmentSeqs
No description
Code
new
No description
Code
Methods description
None available.
Methods code
add_sequencedescriptionprevnextTop
sub add_sequence {
  my ($self, $align_seq) = @_;

  $self->throw("Must attach AlignmentSeq objects to Alignment, not [$align_seq]")
    unless $align_seq->isa("Bio::EnsEMBL::Pipeline::Alignment::AlignmentSeq");

  push (@{$self->{'_alignment_seqs'}}, $align_seq);

  return 1;
}
alignment_namedescriptionprevnextTop
sub alignment_name {
  my $self = shift;

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

  return $self->{'_name'};
}
fetch_AlignmentSeqsdescriptionprevnextTop
sub fetch_AlignmentSeqs {
  my $self = shift;

  return $self->{'_alignment_seqs'};
}

return 1;
}
newdescriptionprevnextTop
sub new {
  my ($class, @args) = @_;

  my $self = bless {},$class;
  
  my ($name, 
      $align_seqs) = rearrange([qw(NAME
				   SEQS)],@args);

  if ($align_seqs) {
    foreach my $align_seq (@$align_seqs){
      $self->add_sequence($align_seq);
    }
  }

  $self->alignment_name($name) if $name;

  return $self;
}
General documentation
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