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Summary

Bio::EnsEMBL::Analysis::PmatchFeature

Package variables

Included modules

Inherit

Synopsis

Description

Methods

Methods description

None available.

Methods code

sub analysis {

   my ($self,$value) = @_;

   if(!$self->{_analysis}){
     $self->{_analysis} = undef;
   }
   if ($value) {
     unless($value->isa('Bio::EnsEMBL::Analysis')) {
       throw("Analysis is not a Bio::EnsEMBL::Analysis object "
		    . "but a $value object");
     }

     $self->{_analysis} = $value;
   } 

   return $self->{_analysis};
}


1;

}

sub cdna_id {

  my ($self,$arg) = @_;

  if (defined($arg)) {
    $self->{_cdna_id} = $arg;
  }

  return $self->{_cdna_id};

}

sub chr_name {

  my ($self,$arg) = @_;

  if (defined($arg)) {
    $self->{_chr_name} = $arg;
  }
  return $self->{_chr_name};

}

sub coverage {

  my ($self,$arg) = @_;

  if (defined($arg)) {

    if ($arg < 0 || $arg > 100) {
      throw("Coverage must be betwee 0 and 100.  Trying to set it to $arg");
    }
    
    $self->{_coverage} = $arg;
  }

  return $self->{_coverage};

}

sub end {

  my ($self,$arg) = @_;

  if (defined($arg)) {
    $self->{_end} = $arg;
  }
  return $self->{_end};

}

sub new {

  my($class,@args) = @_;

  my $self = bless {},$class;
  my ($protein_id,$cdna_id,$chr_name,$start,$end,$coverage,$analysis) = rearrange([qw(PROTEIN_ID 
                       CDNA_ID                                                               CHR_NAME
										 START
										 END
										 COVERAGE
										 ANALYSIS	      
										)],@args);
  
  
  $self->protein_id($protein_id);
  $self->chr_name($chr_name);
  $self->start($start);
  $self->end($end);
  $self->cdna_id($cdna_id);
  $self->coverage($coverage);
  $self->analysis($analysis);
  return $self;

}

sub protein_id {

  my ($self,$arg) = @_;

  if (defined($arg)) {
    $self->{_protein_id} = $arg;
  }

  return $self->{_protein_id};

}

sub score {

   my ($self) = @_ ; 
  return $self->{_coverage};

}

sub start {

  my ($self,$arg) = @_;

  if (defined($arg)) {
    $self->{_start} = $arg;
  }
  return $self->{_start};

}

General documentation