Bio::Search::Hit HMMERHit
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Summary
Bio::Search::Hit::HMMERHit - A Hit module for HMMER hits
Package variables
No package variables defined.
Inherit
Bio::Search::Hit::GenericHit
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.
Methods
next_domainDescriptionCode
domainsDescriptionCode
bitsDescriptionCode
iterationDescriptionCode
Methods description
next_domaincode    nextTop
 Title   : next_domain 
Usage : my $domain = $hit->next_domain();
Function: An alias for next_hsp(), this will return the next HSP
Returns : Bio::Search::HSP::HSPI object
Args : none
domainscodeprevnextTop
 Title   : domains
Usage : my @domains = $hit->domains();
Function: An alias for hsps(), this will return the full list of hsps
Returns : array of Bio::Search::HSP::HSPI objects
Args : none
bitscodeprevnextTop
 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()
iterationcodeprevnextTop
 Title   : iteration
Usage : $obj->iteration($newval)
Function: PSI-BLAST iteration
Returns : value of iteration
Args : newvalue (optional)
Methods code
next_domaindescriptionprevnextTop
sub next_domain {
shift->next_hsp
}
domainsdescriptionprevnextTop
sub domains {
shift->hsps()
}
bitsdescriptionprevnextTop
sub bits {
 return 0
}
iterationdescriptionprevnextTop
sub iteration {
 return 0
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 StajichTop
Email jason@bioperl.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
newTop
 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.
inherited Bio::Search::Hit::GenericHit methodsTop
add_hspTop
 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 methodsTop
nameTop
 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
accessionTop
 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
descriptionTop
 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
lengthTop
 Title   : length
Usage : my $len = $hit->length
Function: Returns the length of the hit
Returns : integer
Args : [optional] integer to set the length
algorithmTop
 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_scoreTop
 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
significanceTop
 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
next_hspTop
 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
hspsTop
 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_hspsTop
 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()
rewindTop
 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