Toolbar

Summary

Bio::Tools::HMMER::Domain - One particular domain hit from HMMER

Package variables

Included modules

Inherit

Bio::SeqFeature::FeaturePair

Synopsis

Read the Bio::Tools::HMMER::Results docs

Description

A particular domain score. We reuse the Homol SeqFeature system
here, so this inherits off Homol SeqFeature. As this code
originally came from a separate project, there are some backward
compatibility stuff provided to keep this working with old code.
Don't forget this inherits off Bio::SeqFeature, so all your usual
nice start/end/score stuff is ready for use.

Methods

Methods description

 Title   : add_alignment_line
 Usage   : $domain->add_alignment_line($line_from_hmmer_output);
 Function: add an alignment line to this Domain object
 Returns : Nothing
 Args    : scalar

 Adds an alignment line, mainly for storing the HMMER alignments
as flat text which can be reguritated. You're right. This is *not
nice* and not the right way to do it.  C'est la vie.

 Title   : bits
 Usage   :
 Function: backward compatibility. Same as score
 Example :
 Returns : 
 Args    :

 Title   : each_alignment_line
 Usage   : foreach $line ( $domain->each_alignment_line )
 Function: reguritates the alignment lines as they were fed in.
           only useful realistically for printing.
 Example :
 Returns : 
 Args    : None

 Title   : evalue
 Usage   :
 Function: $domain->evalue($value);
 Example :
 Returns : 
 Args    :

 Title   : get_nse
 Usage   : $domain->get_nse()
 Function: Provides a seqname/start-end format, useful
           for unique keys. nse stands for name-start-end
           It is used alot in Pfam
 Example :
 Returns : A string
 Args    : Optional seperator 1 and seperator 2 (default / and -)

 Title   : hmm_range
 Usage   :
 Function: Throws an exception to catch scripts which need to upgrade
 Example :
 Returns : 
 Args    :

 Title   : hmmacc
 Usage   : $domain->hmmacc($newacc)
 Function: set get for HMM accession number. This is placed in the homol
           feature of the HMM
 Example :
 Returns : 
 Args    :

 Title   : hmmname
 Usage   : $domain->hmmname($newname)
 Function: set get for HMM accession number. This is placed in the homol
           feature of the HMM
 Example :
 Returns : 
 Args    :

 Title   : seq_range
 Usage   : 
 Function: Throws an exception to catch scripts which need to upgrade
 Example :
 Returns : 
 Args    :

 Title   : seqbits
 Usage   :
 Function: $domain->seqbits($value);
 Example :
 Returns : 
 Args    :

Methods code

sub add_alignment_line {

    my $self = shift;
    my $line = shift;
    push(@{$self->{'alignlines'}},$line);

}

sub bits {

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

   return $self->score($sc);

}

sub each_alignment_line {

    my $self = shift;
    return @{$self->{'alignlines'}};

}

sub end_hmm {

    my $self = shift;
    my $end = shift;

    $self->warn("Using old domain->end_hmm. Should use domain->hend");
    return $self->hend($end);

}

sub end_seq {

    my $self = shift;
    my $end = shift;

    $self->warn("Using old domain->end_seq. Should use domain->end");
    return $self->end($end);
}

#  =head2 start_hmm

#   Title   : start_hmm
#   Usage   : Backward compatibility with old HMMER modules, and
#             for convience. Equivalent to $self->homol_SeqFeature->start
#   Function:
#   Example :
#   Returns : 
#   Args    :

#  =cut

}

sub evalue {

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

   if( defined $value ) {
       $self->add_tag_value('evalue',$value);
   }
   my @vals = $self->each_tag_value('evalue');
   return shift @vals;

}

sub get_nse {

    my $self = shift;
    my $sep1 = shift;
    my $sep2 = shift;

    if( !defined $sep2 ) {
	$sep2 = "-";
    }
    if( !defined $sep1 ) {
	$sep1 = "/";
    }

    return sprintf("%s%s%d%s%d",$self->seq_id,$sep1,$self->start,$sep2,$self->end);
}


#  =head2 start_seq

#   Title   : start_seq
#   Usage   : Backward compatibility with old HMMER modules.
#             should use $domain->start
#   Function:
#   Example :
#   Returns : 
#   Args    :

#  =cut

}

sub hmm_range {

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

   $self->throw("You have accessed an old method. Please recode your script to the new bioperl HMMER module");
}

1;  # says use was ok
__END__

}

sub hmmacc {

   my ($self,$acc) = @_;
   if( defined $acc ) {
       $self->feature2->add_tag_value('accession',$acc);
   }
   my @vals = $self->feature2->each_tag_value('accession');
   return shift @vals;

}

sub hmmname {

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


   if( defined $hname ) {
       $self->hseqname($hname);
   } 

   return $self->hseqname();

}

sub new {

   my($class,@args) = @_;
  my $self = $class->SUPER::new(@args);

  $self->{'alignlines'} = [];

  my $hmmf1 = Bio::SeqFeature::Generic->new(@args);
  my $hmmf2 = Bio::SeqFeature::Generic->new(@args);

  $self->feature1($hmmf1);
  $self->feature2($hmmf2);

  return $self;

}

sub seq_range {

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

   $self->throw("You have accessed an old method. Please recode your script to the new bioperl HMMER module");

}

sub seqbits {

   my ($self,$value) = @_;
   if( defined $value ) {
       $self->add_tag_value('seqbits',$value);
   }
   my @vals = $self->each_tag_value('seqbits');
   return shift @vals;

}

sub start_hmm {

     my $self = shift; 
    my $start = shift; 
    $self->warn("Using old domain->start_hmm. Should use domain->hstart");
    return $self->hstart($start); 
}

#  =head2 end_hmm

#   Title   : end_hmm
#   Usage   : Backward compatibility with old HMMER modules, and
#             for convience. Equivalent to $self->homol_SeqFeature->start
#   Function:
#   Example :
#   Returns : 
#   Args    :

#  =cut

}

sub start_seq {

    my $self = shift;
    my $start = shift;
    
    $self->warn("Using old domain->start_seq. Should use domain->start");
    return $self->start($start);
}

#  =head2 end_seq

#   Title   : end_seq
#   Usage   : Backward compatibility with old HMMER modules.
#             should use $domain->end
#   Function:
#   Example :
#   Returns : 
#   Args    :

#  =cut

}

General documentation

Ewan Birney, birney@ebi.ac.uk

Jason Stajich, jason@bioperl.org

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _