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
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AUTHOR - Jason Stajich
Email [email protected]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)