Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

       Bio::Search::Hit::GenericHit - A generic implementation of the Bio::Search::Hit::HitI
       interface

SYNOPSIS

           use Bio::Search::Hit::GenericHit;
           my $hit = Bio::Search::Hit::GenericHit->new(-algorithm => 'blastp');

           # typically one gets HitI objects from a SearchIO stream via a ResultI
           use Bio::SearchIO;
           my $parser = Bio::SearchIO->new(-format => 'blast', -file => 'result.bls');

           my $result = $parser->next_result;
           my $hit    = $result->next_hit;

       # TODO: Describe how to configure a SearchIO stream so that it generates #
       GenericHit objects.

DESCRIPTION

       This object handles the hit data from a Database Sequence Search such as FASTA or BLAST.

       Unless you're writing a parser, you won't ever need to create a GenericHit 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.

       For documentation on what you can do with GenericHit (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://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich and Steve Chervitz

       Email jason-at-bioperl-dot-org Email sac-at-bioperl-dot-org

CONTRIBUTORS

       Sendu Bala, bix@sendu.me.uk

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::GenericHit->new();
        Function: Builds a new Bio::Search::Hit::GenericHit object
        Returns : Bio::Search::Hit::GenericHit
        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 description

   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 (BLAST2 reports).
        Comments  : Note that the N parameter is not reported in gapped BLAST2.
                  : 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 of the given BLAST hit.
                  : (Note that P-values are not provided with NCBI Blast2 reports).
        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(), significance(), 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()

   logical_length
        Usage     : $hit_object->logical_length( [seq_type] );
                  : (mostly intended for internal use).
        Purpose   : Get the logical length of the hit sequence.
                  : This is necessary since the number of identical/conserved residues
                  : can be in terms of peptide sequence space, yet the query and/or hit
                  : sequence are in nucleotide space.
        Example   : $len    = $hit_object->logical_length();
        Returns   : Integer
        Argument  : seq_type = 'query' or 'hit' or 'sbjct' (default = 'query')
                    ('sbjct' is synonymous with 'hit')
        Throws    : n/a
        Comments  :
                  : In the case of BLAST flavors:
                  : For TBLASTN reports, the length of the aligned portion of the
                  : nucleotide hit sequence is divided by 3; for BLASTX reports,
                  : the length of the aligned portion of the nucleotide query
                  : sequence is divided by 3. For TBLASTX reports, the length of
                  : both hit and query sequence are converted.
                  :
                  : This is important for functions like frac_aligned_query()
                  : which need to operate in amino acid coordinate space when dealing
                  : with [T]BLAST[NX] type reports.

       See Also   : length(), frac_aligned_query(), frac_aligned_hit()

   length_aln
        Usage     : $hit_object->length_aln( [seq_type] );
        Purpose   : Get the total length of the aligned region for query or sbjct seq.
                  : This number will include all HSPs
        Example   : $len    = $hit_object->length_aln(); # default = query
                  : $lenAln = $hit_object->length_aln('query');
        Returns   : Integer
        Argument  : seq_Type = 'query' or 'hit' or 'sbjct' (Default = 'query')
                    ('sbjct' is synonymous with 'hit')
        Throws    : Exception if the argument is not recognized.
        Comments  : This method will report the logical length of the alignment,
                  : meaning that for TBLAST[NX] reports, the length is reported
                  : using amino acid coordinate space (i.e., nucleotides / 3).
                  :
                  : This method requires that all HSPs be tiled. If they have not
                  : already been tiled, they will be tiled first automatically..
                  : If you don't want the tiled data, iterate through each HSP
                  : calling length() on each (use hsps() to get all HSPs).

       See Also   : length(), frac_aligned_query(), frac_aligned_hit(), gaps(),
       Bio::Search::SearchUtils::tile_hsps(), Bio::Search::HSP::BlastHSP::length()

   gaps
        Usage     : $hit_object->gaps( [seq_type] );
        Purpose   : Get the number of gaps in the aligned query, hit, or both sequences.
                  : Data is summed across all HSPs.
        Example   : $qgaps = $hit_object->gaps('query');
                  : $hgaps = $hit_object->gaps('hit');
                  : $tgaps = $hit_object->gaps();    # default = total (query + hit)
        Returns   : scalar context: integer
                  : array context without args: two-element list of integers
                  :    (queryGaps, hitGaps)
                  : Array context can be forced by providing an argument of 'list' or 'array'.
                  :
                  : CAUTION: Calling this method within printf or sprintf is arrray context.
                  : So this function may not give you what you expect. For example:
                  :          printf "Total gaps: %d", $hit->gaps();
                  : Actually returns a two-element array, so what gets printed
                  : is the number of gaps in the query, not the total
                  :
        Argument  : seq_type: 'query' | 'hit' or 'sbjct' | 'total' | 'list'  (default = 'total')
                    ('sbjct' is synonymous with 'hit')
        Throws    : n/a
        Comments  : If you need data for each HSP, use hsps() and then interate
                  : through each HSP object.
                  : This method requires that all HSPs be tiled. If they have not
                  : already been tiled, they will be tiled first automatically..
                  : Not relying on wantarray since that will fail in situations
                  : such as printf "%d", $hit->gaps() in which you might expect to
                  : be printing the total gaps, but evaluates to array context.

       See Also   : length_aln()

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

   start
        Usage     : $sbjct->start( [seq_type] );
        Purpose   : Gets the start coordinate for the query, sbjct, or both sequences
                  : in the BlastHit object. If there is more than one HSP, the lowest start
                  : value of all HSPs is returned.
        Example   : $qbeg = $sbjct->start('query');
                  : $sbeg = $sbjct->start('hit');
                  : ($qbeg, $sbeg) = $sbjct->start();
        Returns   : scalar context: integer
                  : array context without args: list of two integers (queryStart, sbjctStart)
                  : Array context can be "induced" by providing an argument of 'list' or 'array'.
        Argument  : In scalar context: seq_type = 'query' or 'hit' or 'sbjct' (default = 'query')
                    ('sbjct' is synonymous with 'hit')
        Throws    : n/a

       See Also   : end(), range(), strand(),
                    Bio::Search::HSP::BlastHSP::start

   end
        Usage     : $sbjct->end( [seq_type] );
        Purpose   : Gets the end coordinate for the query, sbjct, or both sequences
                  : in the BlastHit object. If there is more than one HSP,
                    the largest end
                  : value of all HSPs is returned.
        Example   : $qend = $sbjct->end('query');
                  : $send = $sbjct->end('hit');
                  : ($qend, $send) = $sbjct->end();
        Returns   : scalar context: integer
                  : array context without args: list of two integers
                  : (queryEnd, sbjctEnd)
                  : Array context can be "induced" by providing an argument
                  : of 'list' or 'array'.
        Argument  : In scalar context: seq_type = 'query' or 'sbjct'
                  :  (case insensitive). If not supplied, 'query' is used.
        Throws    : n/a

       See Also   : start(), range(), strand()

   range
        Usage     : $sbjct->range( [seq_type] );
        Purpose   : Gets the (start, end) coordinates for the query or sbjct sequence
                  : in the HSP alignment.
        Example   : ($qbeg, $qend) = $sbjct->range('query');
                  : ($sbeg, $send) = $sbjct->range('hit');
        Returns   : Two-element array of integers
        Argument  : seq_type = string, 'query' or 'hit' or 'sbjct'  (default = 'query')
                    ('sbjct' is synonymous with 'hit')
        Throws    : n/a

       See Also   : start(), end()

   frac_identical
        Usage     : $hit_object->frac_identical( [seq_type] );
        Purpose   : Get the overall fraction of identical positions across all HSPs.
                  : The number refers to only the aligned regions and does not
                  : account for unaligned regions in between the HSPs, if any.
        Example   : $frac_iden = $hit_object->frac_identical('query');
        Returns   : Float (2-decimal precision, e.g., 0.75).
        Argument  : seq_type: 'query' | 'hit' or 'sbjct' | 'total'
                  : default = 'query' (but see comments below).
                  : ('sbjct' is synonymous with 'hit')
        Throws    : n/a
        Comments  :
                  : To compute the fraction identical, the logical length of the
                  : aligned portion of the sequence is used, meaning that
                  : in the case of BLAST flavors, for TBLASTN reports, the length of
                  : the aligned portion of the
                  : nucleotide hit sequence is divided by 3; for BLASTX reports,
                  : the length of the aligned portion of the nucleotide query
                  : sequence is divided by 3. For TBLASTX reports, the length of
                  : both hit and query sequence are converted.
                  : This is necessary since the number of identical residues is
                  : in terms of peptide sequence space.
                  :
                  : Different versions of Blast report different values for the total
                  : length of the alignment. This is the number reported in the
                  : denominators in the stats section:
                  : "Identical = 34/120 Positives = 67/120".
                  : NCBI BLAST uses the total length of the alignment (with gaps)
                  : WU-BLAST uses the length of the query sequence (without gaps).
                  :
                  : Therefore, when called with an argument of 'total',
                  : this method will report different values depending on the
                  : version of BLAST used. Total does NOT take into account HSP
                  : tiling, so it should not be used.
                  :
                  : To get the fraction identical among only the aligned residues,
                  : ignoring the gaps, call this method without an argument or
                  : with an argument of 'query' or 'hit'.
                  :
                  : If you need data for each HSP, use hsps() and then iterate
                  : through the HSP objects.
                  : This method requires that all HSPs be tiled. If they have not
                  : already been tiled, they will be tiled first automatically.

       See Also   : frac_conserved(), frac_aligned_query(), matches(),
       Bio::Search::SearchUtils::tile_hsps()

   frac_conserved
        Usage     : $hit_object->frac_conserved( [seq_type] );
        Purpose   : Get the overall fraction of conserved positions across all HSPs.
                  : The number refers to only the aligned regions and does not
                  : account for unaligned regions in between the HSPs, if any.
        Example   : $frac_cons = $hit_object->frac_conserved('hit');
        Returns   : Float (2-decimal precision, e.g., 0.75).
        Argument  : seq_type: 'query' | 'hit' or 'sbjct' | 'total'
                  : default = 'query' (but see comments below).
                  : ('sbjct' is synonymous with 'hit')
        Throws    : n/a
        Comments  :
                  : To compute the fraction conserved, the logical length of the
                  : aligned portion of the sequence is used, meaning that
                  : in the case of BLAST flavors, for TBLASTN reports, the length of
                  : the aligned portion of the
                  : nucleotide hit sequence is divided by 3; for BLASTX reports,
                  : the length of the aligned portion of the nucleotide query
                  : sequence is divided by 3. For TBLASTX reports, the length of
                  : both hit and query sequence are converted.
                  : This is necessary since the number of conserved residues is
                  : in terms of peptide sequence space.
                  :
                  : Different versions of Blast report different values for the total
                  : length of the alignment. This is the number reported in the
                  : denominators in the stats section:
                  : "Positives = 34/120 Positives = 67/120".
                  : NCBI BLAST uses the total length of the alignment (with gaps)
                  : WU-BLAST uses the length of the query sequence (without gaps).
                  :
                  : Therefore, when called with an argument of 'total',
                  : this method will report different values depending on the
                  : version of BLAST used. Total does NOT take into account HSP
                  : tiling, so it should not be used.
                  :
                  : To get the fraction conserved among only the aligned residues,
                  : ignoring the gaps, call this method without an argument or
                  : with an argument of 'query' or 'hit'.
                  :
                  : If you need data for each HSP, use hsps() and then interate
                  : through the HSP objects.
                  : This method requires that all HSPs be tiled. If they have not
                  : already been tiled, they will be tiled first automatically.

       See Also   : frac_identical(), matches(), Bio::Search::SearchUtils::tile_hsps()

   frac_aligned_query
        Usage     : $hit_object->frac_aligned_query();
        Purpose   : Get the fraction of the query sequence which has been aligned
                  : across all HSPs (not including intervals between non-overlapping
                  : HSPs).
        Example   : $frac_alnq = $hit_object->frac_aligned_query();
        Returns   : Float (2-decimal precision, e.g., 0.75),
                  : or undef if query length is unknown to avoid division by 0.
        Argument  : n/a
        Throws    : n/a
        Comments  : If you need data for each HSP, use hsps() and then interate
                  : through the HSP objects.
                  : This method requires that all HSPs be tiled. If they have not
                  : already been tiled, they will be tiled first automatically.

       See Also   : frac_aligned_hit(), logical_length(), length_aln(),
       Bio::Search::SearchUtils::tile_hsps()

   frac_aligned_hit
        Usage     : $hit_object->frac_aligned_hit();
        Purpose   : Get the fraction of the hit (sbjct) sequence which has been aligned
                  : across all HSPs (not including intervals between non-overlapping
                  : HSPs).
        Example   : $frac_alnq = $hit_object->frac_aligned_hit();
        Returns   : Float (2-decimal precision, e.g., 0.75),
                  : or undef if hit length is unknown to avoid division by 0.
        Argument  : n/a
        Throws    : n/a
        Comments  : If you need data for each HSP, use hsps() and then interate
                  : through the HSP objects.
                  : This method requires that all HSPs be tiled. If they have not
                  : already been tiled, they will be tiled first automatically.

       See Also   : frac_aligned_query(), matches(), , logical_length(), length_aln(),
       Bio::Search::SearchUtils::tile_hsps()

   frac_aligned_sbjct
       Same as frac_aligned_hit()

   num_unaligned_sbjct
       Same as num_unaligned_hit()

   num_unaligned_hit
        Usage     : $hit_object->num_unaligned_hit();
        Purpose   : Get the number of the unaligned residues in the hit sequence.
                  : Sums across all all HSPs.
        Example   : $num_unaln = $hit_object->num_unaligned_hit();
        Returns   : Integer
        Argument  : n/a
        Throws    : n/a
        Comments  : See notes regarding logical lengths in the comments for frac_aligned_hit().
                  : They apply here as well.
                  : If you need data for each HSP, use hsps() and then interate
                  : through the HSP objects.
                  : This method requires that all HSPs be tiled. If they have not
                  : already been tiled, they will be tiled first automatically..

       See Also   : num_unaligned_query(),  Bio::Search::SearchUtils::tile_hsps(),
       frac_aligned_hit()

   num_unaligned_query
        Usage     : $hit_object->num_unaligned_query();
        Purpose   : Get the number of the unaligned residues in the query sequence.
                  : Sums across all all HSPs.
        Example   : $num_unaln = $hit_object->num_unaligned_query();
        Returns   : Integer
        Argument  : n/a
        Throws    : n/a
        Comments  : See notes regarding logical lengths in the comments for frac_aligned_query().
                  : They apply here as well.
                  : If you need data for each HSP, use hsps() and then interate
                  : through the HSP objects.
                  : This method requires that all HSPs be tiled. If they have not
                  : already been tiled, they will be tiled first automatically..

       See Also   : num_unaligned_hit(), frac_aligned_query(),
       Bio::Search::SearchUtils::tile_hsps()

   seq_inds
        Usage     : $hit->seq_inds( seq_type, class, collapse );
        Purpose   : Get a list of residue positions (indices) across all HSPs
                  : for identical or conserved residues in the query or sbjct sequence.
        Example   : @s_ind = $hit->seq_inds('query', 'identical');
                  : @h_ind = $hit->seq_inds('hit', 'conserved');
                  : @h_ind = $hit->seq_inds('hit', 'conserved', 1);
        Returns   : Array of integers
                  : May include ranges if collapse is non-zero.
        Argument  : [0] seq_type  = 'query' or 'hit' or 'sbjct'  (default = 'query')
                  :                 ('sbjct' is synonymous with 'hit')
                  : [1] class     = 'identical' or 'conserved' (default = 'identical')
                  :              (can be shortened to 'id' or 'cons')
                  :              (actually, anything not 'id' will evaluate to 'conserved').
                  : [2] collapse  = boolean, if non-zero, consecutive positions are merged
                  :             using a range notation, e.g., "1 2 3 4 5 7 9 10 11"
                  :             collapses to "1-5 7 9-11". This is useful for
                  :             consolidating long lists. Default = no collapse.
        Throws    : n/a.

       See Also   : Bio::Search::HSP::BlastHSP::seq_inds()

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

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

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

   sort_hits
        Title          : sort_hsps
        Usage          : $result->sort_hsps(\&sort_function)
        Function       : Sorts the available HSP objects by a user-supplied function. Defaults to sort
                         by descending score.
        Returns        : n/a
        Args           : A coderef for the sort function.  See the documentation on the Perl sort()
                         function for guidelines on writing sort functions.
        Note           : To access the special variables $a and $b used by the Perl sort() function
                         the user function must access Bio::Search::Hit::HitI namespace.
                         For example, use :
                         $hit->sort_hsps( sub{$Bio::Search::Result::HitI::a->length <=>
                                                 $Bio::Search::Result::HitI::b->length});
                          NOT $hit->sort_hsps($a->length <=> $b->length);

   iteration
        Usage     : $hit->iteration( $iteration_num );
        Purpose   : Gets the iteration number in which the Hit was found.
        Example   : $iteration_num = $sbjct->iteration();
        Returns   : Integer greater than or equal to 1
                    Non-PSI-BLAST reports may report iteration as 1, but this number
                    is only meaningful for PSI-BLAST reports.
        Argument  : iteration_num (optional, used when setting only)
        Throws    : none

       See Also   : found_again()

   found_again
        Title     : found_again
        Usage     : $hit->found_again;
                    $hit->found_again(1);
        Purpose   : Gets a boolean indicator whether or not the hit has
                    been found in a previous iteration.
                    This is only applicable to PSI-BLAST reports.

                     This method indicates if the hit was reported in the
                     "Sequences used in model and found again" section of the
                     PSI-BLAST report or if it was reported in the
                     "Sequences not found previously or not previously below threshold"
                     section of the PSI-BLAST report. Only for hits in iteration > 1.

        Example   : if( $hit->found_again()) { ... };
        Returns   : Boolean, true (1) if the hit has been found in a
                    previous PSI-BLAST iteration.
                    Returns false (0 or undef) for hits that have not occurred in a
                    previous PSI-BLAST iteration.
        Argument  : Boolean (1 or 0). Only used for setting.
        Throws    : none

       See Also   : iteration()