Provided by: libbio-perl-perl_1.7.2-2_all bug


       Bio::Search::Hit::ModelHit - A model-based implementation of the Bio::Search::Hit::HitI


           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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AUTHOR - Chris Fields

       Email cjfields at bioperl dot org


       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 description

        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
        Note    : As of Sept. 2016 NCBI records will no longer have a
                  GI; this attributue will remain in place for older

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.