use Bio::Search::Result::HMMERResult;
    my $result = new Bio::Search::Result::HMMERResult
    ( -hmm_name => 'pfam',
      -sequence_file => 'roa1.pep',
      -hits => \@hits);

    # generally we use Bio::SearchIO to build these objects
    use Bio::SearchIO;
    my $in = new Bio::SearchIO(-format => 'hmmer',
			       -file   => 'result.hmmer');
    while( my $result = $in->next_result ) {
	print $result->query_name, " ", $result->algorithm, " ", $result->num_hits(), " hits\n";
    }

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

shift->hits

  my($class,@args) = @_;
  my $self = $class->SUPER::new(@args);
  
  my ($hmm,$seqfile) = $self->_rearrange([qw(HMM_NAME SEQUENCE_FILE)],
					 @args);
  
  defined( $seqfile) && $self->sequence_file($seqfile);
  defined( $hmm) && $self->hmm_name($hmm);

  return $self;

shift->next_hit

   my ($self) = @_;
   $self->{'_hitindex'} = 0;

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

  bioperl-l@bioperl.org              - General discussion
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  bioperl-bugs@bioperl.org
  http://bugzilla.bioperl.org/

 Title   : algorithm
 Usage   : my $r_type = $hsp->algorithm
 Function: Obtain the name of the algorithm used to obtain the Result
 Returns : string (e.g., BLASTP)
 Args    : [optional] scalar string to set value

 Title   : algorithm_version
 Usage   : my $r_version = $hsp->algorithm_version
 Function: Obtain the version of the algorithm used to obtain the Result
 Returns : string (e.g., 2.1.2)
 Args    : [optional] scalar string to set algorithm version value

 Title   : next_hit
 Usage   : while( $hit = $result->next_hit()) { ... }
 Function: Returns the next available Hit object, representing potential
           matches between the query and various entities from the database.
 Returns : a Bio::Search::Hit::HitI object or undef if there are no more.
 Args    : none

 Title   : query_name
 Usage   : $id = $result->query_name();
 Function: Get the string identifier of the query used by the
           algorithm that performed the search.
 Returns : a string.
 Args    : [optional] new string value for query name

 Title   : query_accession
 Usage   : $id = $result->query_accession();
 Function: Get the accession (if available) for the query sequence
 Returns : a string
 Args    : [optional] new string value for accession

 Title   : query_length
 Usage   : $id = $result->query_length();
 Function: Get the length of the query sequence
           used in the search.
 Returns : a number
 Args    :  [optional] new integer value for query length

 Title   : query_description
 Usage   : $id = $result->query_description();
 Function: Get the description of the query sequence
           used in the search.
 Returns : a string
 Args    : [optional] new string for the query description

 Title   : database_name
 Usage   : $name = $result->database_name()
 Function: Used to obtain the name of the database that the query was searched
           against by the algorithm.
 Returns : a scalar string
 Args    : [optional] new string for the db name

 Title   : database_letters
 Usage   : $size = $result->database_letters()
 Function: Used to obtain the size of database that was searched against.
 Returns : a scalar integer (units specific to algorithm, but probably the
           total number of residues in the database, if available) or undef if
           the information was not available to the Processor object.
 Args    : [optional] new scalar integer for number of letters in db

 Title   : database_entries
 Usage   : $num_entries = $result->database_entries()
 Function: Used to obtain the number of entries contained in the database.
 Returns : a scalar integer representing the number of entities in the database
           or undef if the information was not available.
 Args    : [optional] new integer for the number of sequence entries in the db

 Title   : get_parameter
 Usage   : my $gap_ext = $report->get_parameter('gapext')
 Function: Returns the value for a specific parameter used
           when running this report
 Returns : string
 Args    : name of parameter (string)

 Title   : available_parameters
 Usage   : my @params = $report->available_paramters
 Function: Returns the names of the available parameters
 Returns : Return list of available parameters used for this report
 Args    : none

 Title   : get_statistic
 Usage   : my $gap_ext = $report->get_statistic('kappa')
 Function: Returns the value for a specific statistic available 
           from this report
 Returns : string
 Args    : name of statistic (string)

 Title   : available_statistics
 Usage   : my @statnames = $report->available_statistics
 Function: Returns the names of the available statistics
 Returns : Return list of available statistics used for this report
 Args    : none

 Title   : add_hit
 Usage   : $report->add_hit($hit)
 Function: Adds a HitI to the stored list of hits
 Returns : Number of HitI currently stored
 Args    : Bio::Search::Hit::HitI

 Title   : add_parameter
 Usage   : $report->add_parameter('gapext', 11);
 Function: Adds a parameter
 Returns : none
 Args    : key  - key value name for this parama
           value - value for this parameter

 Title   : add_statistic
 Usage   : $report->add_statistic('lambda', 2.3);
 Function: Adds a parameter
 Returns : none
 Args    : key  - key value name for this parama
           value - value for this parameter

 Title   : num_hits
 Usage   : my $hitcount= $result->num_hits
 Function: returns the number of hits for this query result
 Returns : integer
 Args    : none

 Title   : hits
 Usage   : my @hits = $result->hits
 Function: Returns the available hits for this Result
 Returns : Array of Bio::Search::Hit::HitI objects
 Args    : none

 Title   : program_reference
 Usage   : $obj->program_reference($newval)
 Function: 
 Returns : value of the literature reference for the algorithm
 Args    : newvalue (optional)