Bio::Search::Hit::HMMERHit - A Hit module for HMMER hits use Bio::Search::Hit::HMMERHit; my $hit = new Bio::Search::Hit::HMMERHit; # use it in the same way as Bio::Search::Hit::GenericHit 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.

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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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ Email jason@bioperl.org Describe contact details here Additional contributors names and emails here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $obj = new Bio::Search::Hit::HMMERHit(); 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)