Summary

Bio::Tools::HMMER::Set - Set of identical domains from HMMER matches

Package variables

Included modules

Inherit

Bio::Root::Root

Synopsis

    # get a Set object probably from the results object
    print "Bits score over set ",$set->bits," evalue ",$set->evalue,"\n";

    foreach $domain ( $set->each_Domain ) {
	print "Domain start ",$domain->start," end ",$domain->end,"\n";
    }

Description

Represents a set of HMMER domains hitting one sequence. HMMER reports two
different scores, a per sequence total score (and evalue) and a per
domain score and evalue. This object represents a collection of the same
domain with the sequence bits score and evalue. (these attributes are also
on the per domain scores, which you can get there).

Methods

Methods description

 Title   : add_Domain
 Usage   : $set->add_Domain($domain)
 Function: adds the domain to the list
 Returns : nothing
 Args    : A Bio::Tools::HMMER::Domain object

 Title   : each_Domain
 Usage   : foreach $domain ( $set->each_Domain() ) 
 Function: returns an array of domain objects in this set
 Returns : array
 Args    : none

 Title   : name
 Usage   : $obj->name($newval)
 Function: 
 Example : 
 Returns : value of name
 Args    : newvalue (optional)

 Title   : desc
 Usage   : $obj->desc($newval)
 Function: 
 Example : 
 Returns : value of desc
 Args    : newvalue (optional)

 Title   : accession
 Usage   : $obj->accession($newval)
 Function: 
 Example : 
 Returns : value of accession
 Args    : newvalue (optional)

 Title   : bits
 Usage   : $obj->bits($newval)
 Function: 
 Example : 
 Returns : value of bits
 Args    : newvalue (optional)

 Title   : evalue
 Usage   : $obj->evalue($newval)
 Function: 
 Example : 
 Returns : value of evalue
 Args    : newvalue (optional)

Methods code

sub new {

    my($class,@args) = @_;
    my $self = $class->SUPER::new(@args);
    my ($name,$acc,$desc) = $self->_rearrange([qw(NAME ACCESSION DESC)],
					      @args);
    $name && $self->name($name);
    $acc  && $self->accession($acc);
    $desc && $self->desc($desc);

    $self->{'domains'} = [];
    $self->{'domainnames'} = {};
    return $self;

}

sub add_Domain {

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


   if( ! defined $domain || ! $domain->isa("Bio::Tools::HMMER::Domain") ) {
       $self->throw("[$domain] is not a Bio::Tools::HMMER::Domain. aborting");
   }
   return if $self->{'domainnames'}->{$domain->get_nse}++;
   push(@{$self->{'domains'}},$domain);

}

sub each_Domain {

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

   return @{$self->{'domains'}};

}

sub name {

   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'name'} = $value;
    }
    return $obj->{'name'};

}

sub desc {

   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'desc'} = $value;
    }
    return $self->{'desc'};

}

sub accession {

   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'accession'} = $value;
    }
    return $self->{'accession'};

}

sub bits {

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

   if( defined $value) {
      $obj->{'bits'} = $value;
    }
    return $obj->{'bits'};

}

sub evalue {

   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'evalue'} = $value;
    }
    return $obj->{'evalue'};

}

sub addHMMUnit {

    my $self = shift;
    my $unit = shift;

    $self->warn("Using old addHMMUnit call on Bio::Tools::HMMER::Set. Should replace with add_Domain");
    return $self->add_Domain($unit);

}

sub eachHMMUnit {

    my $self = shift;
    $self->warn("Using old eachHMMUnit call on Bio::Tools::HMMER::Set. Should replace with each_Domain");
    return $self->each_Domain();

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org                - General discussion
  http://www.bioperl.org/MailList.html - About the mailing lists

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via email or the web:

  bioperl-bugs@bioperl.org
  http://www.bioperl.org/bioperl-bugs/

Email birney@sanger.ac.uk

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