Bio::Search::Hit::ModelHit(3) A model-based implementation of the Bio::Search::Hit::HitI interface


use Bio::Search::Hit::ModelHit;
my $hit = Bio::Search::Hit::ModelHit->new(-algorithm => 'rnamotif');
# typically one gets HitI objects from a SearchIO stream via a ResultI
use Bio::SearchIO;
my $parser = Bio::SearchIO->new(-format => 'infernal', -file => 'trap.inf');
my $result = $parser->next_result;
my $hit = $result->next_hit;


This object handles the hit data from a database search using models or descriptors instead of sequences, such as Infernal, HMMER, RNAMotif, etc.

Unless you're writing a parser, you won't ever need to create a ModelHit or any other HitI-implementing object. If you use the SearchIO system, HitI objects are created automatically from a SearchIO stream which returns Bio::Search::Hit::HitI objects.

Note that several HitI-based methods have been overridden from ModelHit due to their unreliability when dealing with queries that aren't sequence-based. It may be possible to reimplement these at a later point, but for the time being they will throw warnings and return w/o results.

For documentation on what you can do with ModelHit (and other HitI objects), please see the API documentation in Bio::Search::Hit::HitI.


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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:

AUTHOR - Chris Fields

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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

HitI methods implemented in parent class Bio::Search::Hit::ModelHit


 Title   : new
 Usage   : my $obj = Bio::Search::Hit::ModelHit->new();
 Function: Builds a new Bio::Search::Hit::ModelHit object
 Returns : Bio::Search::Hit::ModelHit
 Args    : -name         => Name of Hit (required)
           -description  => Description (optional)
           -accession    => Accession number (optional)
           -ncbi_gi      => NCBI GI UID (optional)
           -length       => Length of the Hit (optional)
           -score        => Raw Score for the Hit (optional)
           -bits         => Bit 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.
           -found_again  => boolean, true if hit appears in a
                            "previously found" section of a PSI-Blast report.
           -hsp_factory  => Bio::Factory::ObjectFactoryI able to create HSPI


 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, OR hash ref containing data suitable
           for creating a HSPI object (&hsp_factory must be set to get it back)


 Title   : hsp_factory
 Usage   : $hit->hsp_factory($hsp_factory)
 Function: Get/set the factory used to build HSPI objects if necessary.
 Returns : Bio::Factory::ObjectFactoryI
 Args    : Bio::Factory::ObjectFactoryI

Bio::Search::Hit::HitI methods

Implementation of Bio::Search::Hit::HitI methods


 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


 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


 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


 Title   : length
 Usage   : my $len = $hit->length
 Function: Returns the length of the hit
 Returns : integer
 Args    : [optional] integer to set the length


 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


 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


Equivalent to raw_score()


 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


 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
 Comments  : For BLAST1, the non-bit score is listed in the summary line.

See Also : score()


 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


 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 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()


 Usage     : $hit_object->num_hsps();
 Purpose   : Get the number of HSPs for the present hit.
 Example   : $nhsps = $hit_object->num_hsps();
 Returns   : Integer or '-' if HSPs have not been callected
 Argument  : n/a

See Also : hsps()


 Title   : rewind
 Usage   : $hit->rewind;
 Function: Allow one to reset the HSP iterator to the beginning
           Since this is an in-memory implementation
 Returns : none
 Args    : none


 Usage     : $ambig_code = $hit_object->ambiguous_aln();
 Purpose   : Sets/Gets ambiguity code data member.
 Example   : (see usage)
 Returns   : String = 'q', 's', 'qs', '-'
           :   'q'  = query sequence contains overlapping sub-sequences
           :          while sbjct does not.
           :   's'  = sbjct sequence contains overlapping sub-sequences
           :          while query does not.
           :   'qs' = query and sbjct sequence contains overlapping sub-sequences
           :          relative to each other.
           :   '-'  = query and sbjct sequence do not contains multiple domains
           :          relative to each other OR both contain the same distribution
           :          of similar domains.
 Argument  : n/a
 Throws    : n/a
 Comment   : Note: "sbjct" is synonymous with "hit"


See documentation in Bio::Search::Hit::HitI::overlap()


 Usage     : $hit_object->n();
 Purpose   : Gets the N number for the current hit.
           : This is the number of HSPs in the set which was ascribed
           : the lowest P-value (listed on the description line).
           : This number is not the same as the total number of HSPs.
           : To get the total number of HSPs, use num_hsps().
 Example   : $n = $hit_object->n();
 Returns   : Integer
 Argument  : n/a
 Throws    : Exception if HSPs have not been set.
 Comments  : Calling n() on such reports will result in a call to num_hsps().
           : The num_hsps() method will count the actual number of
           : HSPs in the alignment listing, which may exceed N in
           : some cases.

See Also : num_hsps()


 Usage     : $hit_object->p( [format] );
 Purpose   : Get the P-value for the best HSP
 Example   : $p =  $sbjct->p;
           : $p =  $sbjct->p('exp');  # get exponent only.
           : ($num, $exp) =  $sbjct->p('parts');  # split sci notation into parts
 Returns   : Float or scientific notation number (the raw P-value, DEFAULT).
           : Integer if format == 'exp' (the magnitude of the base 10 exponent).
           : 2-element list (float, int) if format == 'parts' and P-value
           :                is in scientific notation (See Comments).
 Argument  : format: string of 'raw' | 'exp' | 'parts'
           :    'raw' returns value given in report. Default. (1.2e-34)
           :    'exp' returns exponent value only (34)
           :    'parts' returns the decimal and exponent as a
           :            2-element list (1.2, -34) (See Comments).
 Throws    : Warns if no P-value is defined. Uses expect instead.
 Comments  : Using the 'parts' argument is not recommended since it will not
           : work as expected if the P-value is not in scientific notation.
           : That is, floats are not converted into sci notation before
           : splitting into parts.

See Also : expect(), signif(), Bio::Search::SearchUtils::get_exponent()


 Usage     : $hit_object->hsp( [string] );
 Purpose   : Get a single HSPI object for the present HitI object.
 Example   : $hspObj  = $hit_object->hsp;  # same as 'best'
           : $hspObj  = $hit_object->hsp('best');
           : $hspObj  = $hit_object->hsp('worst');
 Returns   : Object reference for a object.
 Argument  : String (or no argument).
           :   No argument (default) = highest scoring HSP (same as 'best').
           :   'best' or 'first' = highest scoring HSP.
           :   'worst' or 'last' = lowest scoring HSP.
 Throws    : Exception if the HSPs have not been collected.
           : Exception if an unrecognized argument is used.

See Also : hsps(), num_hsps()


 Title   : rank
 Usage   : $obj->rank($newval)
 Function: Get/Set the rank of this Hit in the Query search list
           i.e. this is the Nth hit for a specific query
 Returns : value of rank
 Args    : newvalue (optional)


 Title   : locus
 Usage   : $locus = $hit->locus();
 Function: Retrieve the locus (if available) for the hit
 Returns : a scalar string (empty string if not set)
 Args    : none


 Title   : each_accession_number
 Usage   : @each_accession_number = $hit->each_accession_number();
 Function: Get each accession number listed in the description of the hit.
           If there are no alternatives, then only the primary accession will
           be given
 Returns : list of all accession numbers in the description
 Args    : none


See documentation in Bio::Search::SearchUtils::tile_hsps()


 Title   : query_length
 Usage   : $obj->query_length($newval)
 Function: Get/Set the query_length
 Returns : value of query_length (a scalar)
 Args    : on set, new value (a scalar or undef, optional)


 Title   : ncbi_gi
 Usage   : $acc = $hit->ncbi_gi();
 Function: Retrieve the NCBI Unique ID (aka the GI #),
           if available, for the hit
 Returns : a scalar string (empty string if not set)
 Args    : none

ModelHit methods overridden in ModelHit

The following methods have been overridden due to their current reliance on sequence-based queries. They may be implemented in future versions of this class.