Bio::Search::Hit::HMMERHit(3pm) 			User Contributed Perl Documentation			   Bio::Search::Hit::HMMERHit(3pm)

NAME

       Bio::Search::Hit::HMMERHit - A Hit module for HMMER hits

SYNOPSIS

	   use Bio::Search::Hit::HMMERHit;
	   my $hit = Bio::Search::Hit::HMMERHit->new();
	   # use it in the same way as Bio::Search::Hit::GenericHit

DESCRIPTION

       This is a specialization of Bio::Search::Hit::GenericHit.  There are a few news methods next_domain and domains.  Note that bits and
       iteration make no sense for this object and will return 0.

FEEDBACK

   Mailing Lists
       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

   Support
       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.

   Reporting Bugs
       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/

AUTHOR - Jason Stajich
       Email jason@bioperl.org

APPENDIX

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

   new
	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.

   next_domain
	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

   domains
	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

   inherited Bio::Search::Hit::GenericHit methods
   add_hsp
	Title	: add_hsp
	Usage	: $hit->add_hsp($hsp)
	Function: Add a HSP to the collection of HSPs for a Hit
	Returns : number of HSPs in the Hit
	Args	: Bio::Search::HSP::HSPI object

   Bio::Search::Hit::HitI methods
   name
	Title	: name
	Usage	: $hit_name = $hit->name();
	Function: returns the name of the Hit sequence
	Returns : a scalar string
	Args	: [optional] scalar string to set the name

   accession
	Title	: accession
	Usage	: $acc = $hit->accession();
	Function: Retrieve the accession (if available) for the hit
	Returns : a scalar string (empty string if not set)
	Args	: none

   description
	Title	: description
	Usage	: $desc = $hit->description();
	Function: Retrieve the description for the hit
	Returns : a scalar string
	Args	: [optional] scalar string to set the descrition

   length
	Title	: length
	Usage	: my $len = $hit->length
	Function: Returns the length of the hit
	Returns : integer
	Args	: [optional] integer to set the length

   algorithm
	Title	: algorithm
	Usage	: $alg = $hit->algorithm();
	Function: Gets the algorithm specification that was used to obtain the hit
		  For BLAST, the algorithm denotes what type of sequence was aligned
		  against what (BLASTN: dna-dna, BLASTP prt-prt, BLASTX translated
		  dna-prt, TBLASTN prt-translated dna, TBLASTX translated
		  dna-translated dna).
	Returns : a scalar string
	Args	: [optional] scalar string to set the algorithm

   raw_score
	Title	: raw_score
	Usage	: $score = $hit->raw_score();
	Function: Gets the "raw score" generated by the algorithm.  What
		  this score is exactly will vary from algorithm to algorithm,
		  returning undef if unavailable.
	Returns : a scalar value
	Args	: [optional] scalar value to set the raw score

   significance
	Title	: significance
	Usage	: $significance = $hit->significance();
	Function: Used to obtain the E or P value of a hit, i.e. the probability that
		  this particular hit was obtained purely by random chance.  If
		  information is not available (nor calculatable from other
		  information sources), return undef.
	Returns : a scalar value or undef if unavailable
	Args	: [optional] scalar value to set the significance

   bits
	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()

   next_hsp
	Title	 : next_hsp
	Usage	 : while( $hsp = $obj->next_hsp()) { ... }
	Function : Returns the next available High Scoring Pair
	Example  :
	Returns  : Bio::Search::HSP::HSPI object or null if finished
	Args	 : none

   hsps
	Usage	  : $hit_object->hsps();
	Purpose   : Get a list containing all HSP objects.
		  : Get the numbers of HSPs for the current hit.
	Example   : @hsps = $hit_object->hsps();
		  : $num  = $hit_object->hsps();  # alternatively, use num_hsps()
	Returns   : Array context : list of Bio::Search::HSP::BlastHSP.pm objects.
		  : Scalar context: integer (number of HSPs).
		  :		    (Equivalent to num_hsps()).
	Argument  : n/a. Relies on wantarray
	Throws	  : Exception if the HSPs have not been collected.

       See Also   : hsp(), num_hsps()

   num_hsps
	Usage	  : $hit_object->num_hsps();
	Purpose   : Get the number of HSPs for the present Blast hit.
	Example   : $nhsps = $hit_object->num_hsps();
	Returns   : Integer
	Argument  : n/a
	Throws	  : Exception if the HSPs have not been collected.

       See Also   : hsps()

   rewind
	Title	: rewind
	Usage	: $hit->rewind;
	Function: Allow one to reset the HSP iteration to the beginning
		  Since this is an in-memory implementation
	Returns : none
	Args	: none

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

perl v5.14.2							    2012-03-02					   Bio::Search::Hit::HMMERHit(3pm)