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Bio::Search::Hit::HMMERHit.3pm

NAME

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

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

Mailing Lists

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

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 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 the web:

   http://bugzilla.open-bio.org/
 
 

AUTHOR - Jason Stajich

Email jason@bioperl.org

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)