Bio::Search::Hit::hmmer3Hit(3) DESCRIPTION of Object


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


 Title   : new
 Usage   : my $obj = Bio::Search::Hit::HMMERHit->new();
 Function: Builds a new Bio::Search::Hit::HMMERHit object 
 Returns : Bio::Search::Hit::HMMERHit
 Args    : 
 Plus the Bio::Search::Hit::GenericHit inherited params
           -name         => Name of Hit (required)
           -description  => Description (optional)
           -accession    => Accession number (optional)
           -length       => Length of the Hit (optional)
           -score        => Raw Score for the Hit (optional)
           -significance => Significance value for the Hit (optional)
           -algorithm    => Algorithm used (BLASTP, FASTX, etc...)
           -hsps         => Array ref of HSPs for this Hit.


 Title   : next_domain 
 Usage   : my $domain = $hit->next_domain();
 Function: An alias for L<next_hsp()>, this will return the next HSP
 Returns : L<Bio::Search::HSP::HSPI> object
 Args    : none


 Title   : domains
 Usage   : my @domains = $hit->domains();
 Function: An alias for L<hsps()>, this will return the full list of hsps
 Returns : array of L<Bio::Search::HSP::HSPI> objects
 Args    : none


 Usage     : $hit_object->bits();
 Purpose   : Gets the bit score of the best HSP for the current hit.
 Example   : $bits = $hit_object->bits();
 Returns   : Integer or undef if bit score is not set
 Argument  : n/a

See Also : score()


 Title   : iteration
 Usage   : $obj->iteration($newval)
 Function: PSI-BLAST iteration
 Returns : value of iteration
 Args    : newvalue (optional)