hmmer documentation.

    # do not use this class directly it is available through Bio::SearchIO
    use Bio::SearchIO;
    my $in = Bio::SearchIO->new(-format => 'hmmer',
                               -file   => 't/data/L77119.hmmer');
    while( my $result = $in->next_result ) {
        # this is a Bio::Search::Result::HMMERResult object
        print $result->query_name(), " for HMM ", $result->hmm_name(), "\n";
        while( my $hit = $result->next_hit ) {
            print $hit->name(), "\n";
            while( my $hsp = $hit->next_hsp ) {
                print "length is ", $hsp->length(), "\n";
            }
        }
    }

sub new {

  my ( $caller, @args ) = @_;
  my $class = ref($caller) || $caller;

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

  # Try to guess the hmmer format version if it's not specified.
  my $version;
  my %param = @args;

  @param{ map { lc $_ } keys %param } = values %param; # lowercase keys

  # If the caller specified a version, go for that
  if (defined($param{"-version"})) {
    $version = $param{"-version"};
  } else {

    # read second line of the file
    my $first_line = $self->_readline;
    $_ = $self->_readline;

    if ( m/HMMER\s3/ ) {
      $version = "3";
    } else {
      $version = "2";
    }

    $self->_pushback($_);
    $self->_pushback($first_line);
  }

  my $format = "hmmer$version";
  return unless( $class->_load_format_module($format) );

  bless($self, "Bio::SearchIO::$format");

  return $self;

}

sub _initialize {

    my ( $self, @args ) = @_;
    $self->SUPER::_initialize(@args);
    my $handler = $self->_eventHandler;
    $handler->register_factory(
        'result',
        Bio::Factory::ObjectFactory->new(
            -type      => 'Bio::Search::Result::HMMERResult',
            -interface => 'Bio::Search::Result::ResultI'
        )
    );

    $handler->register_factory(
        'hit',
        Bio::Factory::ObjectFactory->new(
            -type      => 'Bio::Search::Hit::HMMERHit',
            -interface => 'Bio::Search::Hit::HitI'
        )
    );

    $handler->register_factory(
        'hsp',
        Bio::Factory::ObjectFactory->new(
            -type      => 'Bio::Search::HSP::HMMERHSP',
            -interface => 'Bio::Search::HSP::HSPI'
        )
    );
}

1;

}

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

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.

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

  https://redmine.open-bio.org/projects/bioperl/

new	No description	Code
_initialize	No description	Code