/ 
bioperl-1.4
/ Bio::Search::Hit::HMMERHit

NAME

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

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.

FEEDBACK

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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 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/

AUTHOR - Jason Stajich

Email jason@bioperl.org

Describe contact details here

CONTRIBUTORS

Additional contributors names and emails here

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 = 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)