Bio::Search::Hit HMMERHit
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Search::Hit::HMMERHit - A Hit module for HMMER hits
Package variables
No package variables defined.
Included modules
Bio::Search::Hit::GenericHit
Inherit
Bio::Search::Hit::GenericHit
Synopsis
    use Bio::Search::Hit::HMMERHit;
    my $hit = new Bio::Search::Hit::HMMERHit;
    # 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/MailList.shtml  - About the mailing lists
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
email or the web:
  bioperl-bugs@bioperl.org
  http://bugzilla.bioperl.org/
AUTHOR - Jason StajichTop
Email jason@bioperl.org
Describe contact details here
CONTRIBUTORSTop
Additional contributors names and emails here
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 = 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.
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