Summary

Bio::Search::Hit::Fasta - Hit object specific for Fasta-generated hits

Package variables

Inherit

Bio::Search::Hit::HitI

Synopsis

  # You wouldn't normally create these manually; 
  # instead they would be produced by Bio::SearchIO::fasta

  use Bio::Search::Hit::Fasta;
  my $hit = Bio::Search::Hit::Fasta->new(id=>'LBL_6321', desc=>'lipoprotein', e_val=>0.01);

Description

Bio::Search::Hit::HitI objects are data structures that contain information
about specific hits obtained during a library search. Some information will
be algorithm-specific, but others will be generally defined, such as the
ability to obtain alignment objects corresponding to each hit.

Methods

Methods description

 Function: where the heavy stuff will happen when new is called

 Function: Provide getter/setters for ID,DESC,SIZE,INITN,INIT1,OPT,ZSC,E_VAL

Methods code

sub _initialize {

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

    my $make = $self->SUPER::_initialize(%args);

    while (my ($key, $val) = each %args) {
	$key = '_' . uc($key);
	$self->$key($val);
    }

    return $make; # success - we hope!

}

sub AUTOLOAD {

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

    $AUTOLOAD =~ s/.*:://;

    if ( $AUTOLOAD_OK{$AUTOLOAD} ) {
        $self->{$AUTOLOAD} = $val if defined $val;
        return $self->{$AUTOLOAD};
    } else {
        $self->throw("Unallowed accessor: $AUTOLOAD !");
    }

}

General documentation

Bio::Search::Hit::HitI,
Bio::Search::Hit::GenericHit,
Bio::SearchIO::fasta.

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.

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

  http://bugzilla.open-bio.org/

Email amackey-at-virginia.edu

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