Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

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

SYNOPSIS

           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;

DESCRIPTION

       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.

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:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Chris Fields

       Email cjfields at bioperl dot org

APPENDIX

       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

   new
        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
                                   objects.

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

   hsp_factory
        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

   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

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

       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 hit.
        Example   : $nhsps = $hit_object->num_hsps();
        Returns   : Integer or '-' if HSPs have not been callected
        Argument  : n/a

       See Also   : hsps()

   rewind
        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

   ambiguous_aln
        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"

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

   n
        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()

   p
        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()

   hsp
        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 Bio::Search::HSP::BlastHSP.pm 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()

   rank
        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)

   locus
        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

   each_accession_number
        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

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

   query_length
        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)

   ncbi_gi
        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.

   length_aln
   gaps
   matches
   start
   end
   range
   frac_identical
   frac_conserved
   frac_aligned_query
   frac_aligned_hit
   num_unaligned_hit
   num_unaligned_query
   seq_inds
   strand
   frame
   logical_length