maint: remove Travis stuff which has been replaced with Github actions (#325)

[bioperl-live.git] / lib / Bio / Search / Hit / GenericHit.pm

#
# BioPerl module for Bio::Search::Hit::GenericHit
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

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

=head1 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.

=head1 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
L<Bio::Search::Hit::HitI|Bio::Search::Hit::HitI>.

=head1 FEEDBACK

=head2 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

=head2 Support 

Please direct usage questions or support issues to the mailing list:

I<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.

=head2 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

=head1 AUTHOR - Jason Stajich and Steve Chervitz

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

=head1 CONTRIBUTORS

Sendu Bala, bix@sendu.me.uk

=head1 APPENDIX

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

=cut


# Let the code begin...


package Bio::Search::Hit::GenericHit;

use strict;

use Bio::Search::SearchUtils;

use base qw(Bio::Root::Root Bio::Search::Hit::HitI);

=head2 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.

=cut

sub new {
  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  my ($hsps, $name,$query_len,$desc, $acc, $locus, $length,
      $score,$algo,$signif,$bits, $p,
      $rank, $hsp_factory, $gi, $iter, $found) = $self->_rearrange([qw(HSPS
                                     NAME 
                                     QUERY_LEN
                                     DESCRIPTION
                                     ACCESSION
                                     LOCUS
                                     LENGTH SCORE ALGORITHM 
                                     SIGNIFICANCE BITS P
                                     RANK
                                     HSP_FACTORY
                                     NCBI_GI
                                     ITERATION
                                     FOUND_AGAIN)], @args);
  
  defined $query_len && $self->query_length($query_len);

  if( ! defined $name ) { 
      $self->throw("Must have defined a valid name for Hit");
  } else { 
      $self->name($name);
  }  

  defined $acc         && $self->accession($acc);
  defined $locus       && $self->locus($locus);
  defined $desc        && $self->description($desc);
  defined $length      && $self->length($length);
  defined $algo        && $self->algorithm($algo);
  defined $signif      && $self->significance($signif);
  defined $score       && $self->raw_score($score);
  defined $bits        && $self->bits($bits);
  defined $rank        && $self->rank($rank);
  defined $hsp_factory && $self->hsp_factory($hsp_factory);
  defined $gi          && $self->ncbi_gi($gi);
  defined $iter        && $self->iteration($iter);
  defined $found       && $self->found_again($found);  
  # p() has a weird interface, so this is a hack workaround
  if (defined $p) {
      $self->{_p} = $p;
  }

  $self->{'_iterator'} = 0;
  if( defined $hsps  ) {
      if( ref($hsps) !~ /array/i ) {
          $self->warn("Did not specify a valid array ref for the param HSPS ($hsps)");
      } else {
          my $hspcount=0;
          while( @{$hsps} ) { 
              $hspcount++;
              $self->add_hsp(shift @{$hsps} );
          }
          $self->{'_hsps'} = undef if $hspcount == 0;
      }
  } 
  else {
      $self->{'_hsps'} = undef;
  }

  return $self;
}

=head2 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)

=cut

sub add_hsp {
   my ($self,$hsp) = @_;
   if (!defined $hsp || (ref($hsp) ne 'HASH' && !$hsp->isa('Bio::Search::HSP::HSPI'))) { 
       $self->throw("Must provide a valid Bio::Search::HSP::HSPI object or hash ref to object: $self method: add_hsp value: $hsp");
       return;
   }
   
   push @{$self->{'_hsps'}}, $hsp;
   if (ref($hsp) eq 'HASH') {
       $self->{_hashes}->{$#{$self->{'_hsps'}}} = 1;
   }
   return scalar @{$self->{'_hsps'}};
}

=head2 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

=cut

sub hsp_factory {
    my $self = shift;
    if (@_) { $self->{_hsp_factory} = shift }
    return $self->{_hsp_factory} || return;
}

=head2 Bio::Search::Hit::HitI methods

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

=head2 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

=cut

sub name {
    my ($self,$value) = @_;
    my $previous = $self->{'_name'};
    if( defined $value || ! defined $previous ) {
        $value = $previous = '' unless defined $value;
        $self->{'_name'} = $value;
    } 
    return $previous;
}

=head2 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

=cut

sub accession {
    my ($self,$value) = @_;
    my $previous = $self->{'_accession'};
    if( defined $value || ! defined $previous ) { 
        $value = $previous = '' unless defined $value;
        $self->{'_accession'} = $value;
    } 
        return $previous;
}

=head2 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

=cut

sub description {
    my ($self,$value) = @_;
    my $previous = $self->{'_description'};
    if( defined $value || ! defined $previous ) { 
        $value = $previous = '' unless defined $value;
        $self->{'_description'} = $value;
    } 
    return $previous;
}

=head2 length

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

=cut

sub length {
    my ($self,$value) = @_;
    my $previous = $self->{'_length'};
    if( defined $value || ! defined $previous ) { 
        $value = $previous = 0 unless defined $value;
        $self->{'_length'} = $value;
    } 
    return $previous;
}


=head2 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

=cut

sub algorithm {
    my ($self,$value) = @_;
    my $previous = $self->{'_algorithm'};
    if( defined $value || ! defined $previous ) { 
        $value = $previous = '' unless defined $value;
        $self->{'_algorithm'} = $value;
    } 
    return $previous;
}

=head2 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

=cut

sub raw_score {
    my ($self,$value) = @_; 
    my $previous = $self->{'_score'};
    if( defined $value ) { 
        $self->{'_score'} = $value;
    } elsif ( ! defined $previous ) {
        # Set the bits of the Hit to that of the top HSP.
        unless( defined $self->{'_hsps'}->[0] ) {
            $self->warn("No HSPs for this minimal Hit (".$self->name.")\n".
                    "If using NCBI BLAST, check bits() instead");
            return;
        }
        # use 'score' if available
        if ( defined( ($self->hsps)[0]->score ) ) {
            $previous = $self->{'_score'} = ($self->hsps)[0]->score;
        }
        # otherwise use 'bits'
        elsif ( defined( ($self->hsps)[0]->bits ) ) {
             $previous = $self->{'_score'} = ($self->hsps)[0]->bits;
        }
    }    
    return $previous;
}

=head2 score

Equivalent to L<raw_score()|raw_score>

=cut

sub score { shift->raw_score(@_); }

=head2 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

=cut

sub significance {
    my ($self,$value) = @_;
    my $previous = $self->{'_significance'};
    if( defined $value ) { 
        $self->{'_significance'} = $value;
    } elsif ( ! defined $previous ) {
        unless( defined $self->{'_hsps'}->[0] ) {
            $self->warn("No HSPs for this Hit (".$self->name.")");
            return;
        }
        # Set the significance of the Hit to that of the top HSP.
        $previous = $self->{'_significance'} = ($self->hsps)[0]->significance;
    }

    return $previous;
}

=head2 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   : L<score()|score>

=cut

sub bits {
    my ($self,$value) = @_; 
    my $previous = $self->{'_bits'};
    if( defined $value ) { 
        $self->{'_bits'} = $value;
    } elsif ( ! defined $previous ) {
        # Set the bits of the Hit to that of the top HSP.
        unless( defined $self->{'_hsps'}->[0] ) {
            $self->warn("No HSPs for this minimal Hit (".$self->name.")\n".
                    "If using WU-BLAST, check raw_score() instead");
            return;
        }
        $previous = $self->{'_bits'} = ($self->hsps)[0]->bits;
    }    
    return $previous;
}

=head2 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

=cut

sub next_hsp {
    my $self = shift;
    $self->{'_iterator'} = 0 unless defined $self->{'_iterator'};
    return unless
        defined($self->{'_hsps'}) 
        && $self->{'_iterator'} <= scalar @{$self->{'_hsps'}};
    
    my $iterator = $self->{'_iterator'}++;
    my $hsp = $self->{'_hsps'}->[$iterator] || return;
    if (ref($hsp) eq 'HASH') {
        my $factory = $self->hsp_factory || $self->throw("Tried to get a HSP, but it was a hash ref and we have no hsp factory");
        $hsp = $factory->create_object(%{$hsp});
        $self->{'_hsps'}->[$iterator] = $hsp;
        delete $self->{_hashes}->{$iterator};
    }
    return $hsp;  
}


=head2 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   : L<hsp()|hsp>, L<num_hsps()|num_hsps>

=cut

sub hsps {
    my $self = shift;
    foreach my $i (keys %{$self->{_hashes} || {}}) {
        my $factory = $self->hsp_factory || $self->throw("Tried to get a HSP, but it was a hash ref and we have no hsp factory");
        $self->{'_hsps'}->[$i] = $factory->create_object(%{$self->{'_hsps'}->[$i]});
        delete $self->{_hashes}->{$i};
    }
    
    return wantarray() ? @{$self->{'_hsps'} || []} : scalar(@{$self->{'_hsps'} || []});
}

=head2 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   : L<hsps()|hsps>

=cut

sub num_hsps {
    my $self = shift;
    
    unless ($self->{'_hsps'}) {
        return '-';
    }
    
    return scalar(@{$self->{'_hsps'}});
}

=head2 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

=cut

sub rewind{
   my ($self) = @_;
   $self->{'_iterator'} = 0;
}

=head2 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"

=cut

sub ambiguous_aln {
    my $self = shift;
    if(@_) { $self->{'_ambiguous_aln'} = shift; }
    $self->{'_ambiguous_aln'} || '-';
}

=head2 overlap

See documentation in L<Bio::Search::Hit::HitI::overlap()|Bio::Search::Hit::HitI>

=cut

sub overlap {
    my $self = shift; 
    if(@_) { $self->{'_overlap'} = shift; }
    defined $self->{'_overlap'} ? $self->{'_overlap'} : 0;
}


=head2 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   : L<num_hsps()|num_hsps>

=cut

sub n {
    my $self = shift; 

    # The check for $self->{'_n'} is a remnant from the 'query' mode days
    # in which the sbjct object would collect data from the description 
    # line only.

    my ($n);
    if(not defined($self->{'_n'})) {
        if( $self->hsp ) {
            $n = $self->hsp->n;
        }
    } else {
        $n = $self->{'_n'}; 
    } 
    $n ||= $self->num_hsps;

    return $n;
}

=head2 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   : L<expect()|expect>, L<significance()|significance>, L<Bio::Search::SearchUtils::get_exponent()|Bio::Search::SearchUtils>

=cut

sub p {
# Some duplication of logic for p(), expect() and signif() for the sake of performance.
    my ($self, $fmt) = @_;

    my $val = $self->{'_p'};

    # $val can be zero.
    if(!defined $val) {
        # P-value not defined, must be a NCBI Blast2 report.
        # Use expect instead.
        $self->warn( "P-value not defined. Using significance() instead.");
        $val = $self->significance();
    }

    return $val if not $fmt or $fmt =~ /^raw/i;
    ## Special formats: exponent-only or as list.
    return &Bio::Search::SearchUtils::get_exponent($val) if $fmt =~ /^exp/i;
    return (split (/eE/, $val)) if $fmt =~ /^parts/i;

    ## Default: return the raw P-value.
    return $val;
}

=head2 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   : L<hsps()|hsps>, L<num_hsps>()

=cut

sub hsp {
    my( $self, $option ) = @_;
    $option ||= 'best';
    
    if (not ref $self->{'_hsps'}) {
        $self->throw("Can't get HSPs: data not collected.");
    }

    my @hsps = $self->hsps;
    
    return $hsps[0]      if $option =~ /best|first|1/i;
    return $hsps[$#hsps] if $option =~ /worst|last/i;

    $self->throw("Can't get HSP for: $option\n" .
                 "Valid arguments: 'best', 'worst'");
}

=head2 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   : L<length()|length>, L<frac_aligned_query()|frac_aligned_query>, L<frac_aligned_hit()|frac_aligned_hit>

=cut

sub logical_length {
    my $self = shift;
    my $seqType = shift || 'query';
    $seqType = 'sbjct' if $seqType eq 'hit';

    my ($length, $logical);
    my $algo = $self->algorithm;

    # For the sbjct, return logical sbjct length
    if( $seqType eq 'sbjct' ) {
        $length = $self->length;
    } else {
        # Otherwise, return logical query length
        $length = $self->query_length();
    }

    $logical = Bio::Search::SearchUtils::logical_length($algo, $seqType, $length);

    return int($logical);
}

=head2 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   : L<length()|length>, L<frac_aligned_query()|frac_aligned_query>, L<frac_aligned_hit()|frac_aligned_hit>, L<gaps()|gaps>, L<Bio::Search::SearchUtils::tile_hsps()|Bio::Search::SearchUtils>, L<Bio::Search::HSP::BlastHSP::length()|Bio::Search::HSP::BlastHSP>

=cut

sub length_aln {
    my( $self, $seqType, $num ) = @_;

    $seqType ||= 'query';
    $seqType = 'sbjct' if $seqType eq 'hit';

    # Setter:
    if( defined $num) {
        return $self->{'_length_aln_'.$seqType} = $num;
    }

    unless ($self->{'_hsps'}) {
        #return wantarray ? ('-','-') : '-';
        Bio::Search::SearchUtils::_warn_about_no_hsps($self);
        return '-';
    }

    Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps;

    my $data = $self->{'_length_aln_'.$seqType};
    
    ## If we don't have data, figure out what went wrong.
    if(!$data) {
        $self->throw("Can't get length aln for sequence type \"$seqType\". " . 
                     "Valid types are 'query', 'hit', 'sbjct' ('sbjct' = 'hit')");
    }                
    return $data;
}    

=head2 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   : L<length_aln()|length_aln>

=cut

sub gaps {
    my( $self, $seqType, $num ) = @_;

    $seqType ||= (wantarray ? 'list' : 'total');
    $seqType = 'sbjct' if $seqType eq 'hit';

    unless ($self->{'_hsps'}) {
        Bio::Search::SearchUtils::_warn_about_no_hsps($self);
        return wantarray ? ('-','-') : '-';
        #return '-';
    }

    Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps;

    $seqType = lc($seqType);

    if( defined $num ) {
        $self->throw("Can't set gaps for seqType '$seqType'. Must be 'query' or 'hit'\n") unless ($seqType eq 'sbjct' or $seqType eq 'query');

        return $self->{'_gaps_'.$seqType} = $num;
    }
    elsif($seqType =~ /list|array/i) {
        return ($self->{'_gaps_query'}, $self->{'_gaps_sbjct'});
    }
    elsif($seqType eq 'total') {
        return ($self->{'_gaps_query'} + $self->{'_gaps_sbjct'}) || 0;
    } else {
        return $self->{'_gaps_'.$seqType} || 0;
    }
}    


=head2 matches

See documentation in L<Bio::Search::Hit::HitI::matches()|Bio::Search::Hit::HitI>

=cut

sub matches {
    my( $self, $arg1, $arg2) = @_;
    my(@data,$data);

    unless ($self->{'_hsps'}) {
        Bio::Search::SearchUtils::_warn_about_no_hsps($self);
        return wantarray ? ('-','-') : '-';
    }

    Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps;

    unless( $arg1 ) {
        @data = ($self->{'_totalIdentical'}, $self->{'_totalConserved'});

        return @data;
    } else {

        if( defined $arg2 ) {
            $self->{'_totalIdentical'} = $arg1;
            $self->{'_totalConserved'} = $arg2;
            return ( $arg1, $arg2 );
        }
        elsif($arg1 =~ /^id/i) { 
            $data = $self->{'_totalIdentical'};
        } else {
            $data = $self->{'_totalConserved'};
        }
        #print STDERR "\nmatches(): id=$self->{'_totalIdentical'}, cons=$self->{'_totalConserved'}\n\n";
        return $data;
    }
    
    ## If we make it to here, it is likely the case that
    ## the parser constructed a minimal hit object from the summary line only.
    ## It either delibrately skipped parsing the alignment section,
    ## or was not able to because it was absent (due to blast executable parameter
    ## setting such as -b 0 (B=0 for WU-BLAST) )
    #$self->throw("Can't get identical or conserved data: no data.");
}


=head2 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   : L<end()|end>, L<range()|range>, L<strand()|strand>, 
             L<Bio::Search::HSP::BlastHSP::start|Bio::Search::HSP::BlastHSP>

=cut

sub start {
    my ($self, $seqType, $num) = @_;

    unless ($self->{'_hsps'}) {
        Bio::Search::SearchUtils::_warn_about_no_hsps($self);
        return wantarray ? ('-','-') : '-';
    }

    $seqType ||= (wantarray ? 'list' : 'query');
    $seqType = 'sbjct' if $seqType eq 'hit';

    if( defined $num ) {
        $seqType = "_\L$seqType\E";
        return $self->{$seqType.'Start'} = $num;
    }

    # If there is only one HSP, defer this call to the solitary HSP.
    if($self->num_hsps == 1) {
        return $self->hsp->start($seqType);
    }
    else {
        # Tiling normally generates $self->{'_queryStart'} and
        # $self->{'_sbjctStart'}, but is very slow. If we haven't tiled,
        # find the answer quickly without tiling.
        unless (defined $self->{'_queryStart'}) {
            my $earliest_query_start;
            my $earliest_sbjct_start;
            foreach my $hsp ($self->hsps) {
                my $this_query_start = $hsp->start('query');
                if (! defined $earliest_query_start || $this_query_start < $earliest_query_start) {
                    $earliest_query_start = $this_query_start;
                }
                
                my $this_sbjct_start = $hsp->start('sbjct');
                if (! defined $earliest_sbjct_start || $this_sbjct_start < $earliest_sbjct_start) {
                    $earliest_sbjct_start = $this_sbjct_start;
                }
            }
            $self->{'_queryStart'} = $earliest_query_start;
            $self->{'_sbjctStart'} = $earliest_sbjct_start;
        }
        
        
        if ($seqType =~ /list|array/i) {
            return ($self->{'_queryStart'}, $self->{'_sbjctStart'});
        } else {
            ## Sensitive to member name changes.
            $seqType = "_\L$seqType\E";
            return $self->{$seqType.'Start'};
        }
    }
}


=head2 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   : L<start()|start>, L<range()|range>, L<strand()|strand>

=cut

sub end {
    my ($self, $seqType, $num) = @_;

    unless ($self->{'_hsps'}) {
        return wantarray ? ('-','-') : '-';
    }

    $seqType ||= (wantarray ? 'list' : 'query');
    $seqType = 'sbjct' if $seqType eq 'hit';

    if( defined $num ) {
        $seqType = "_\L$seqType\E";
        return $self->{$seqType.'Stop'} = $num;
    }

    # If there is only one HSP, defer this call to the solitary HSP.
    if($self->num_hsps == 1) {
        return $self->hsp->end($seqType);
    }
    else {
        # Tiling normally generates $self->{'_queryStop'} and
        # $self->{'_sbjctStop'}, but is very slow. If we haven't tiled,
        # find the answer quickly without tiling.
        unless (defined $self->{'_queryStop'}) {
            my $latest_query_end;
            my $latest_sbjct_end;
            foreach my $hsp ($self->hsps) {
                my $this_query_end = $hsp->end('query');
                if (! defined $latest_query_end || $this_query_end > $latest_query_end) {
                    $latest_query_end = $this_query_end;
                }
                
                my $this_sbjct_end = $hsp->end('sbjct');
                if (! defined $latest_sbjct_end || $this_sbjct_end > $latest_sbjct_end) {
                    $latest_sbjct_end = $this_sbjct_end;
                }
            }
            $self->{'_queryStop'} = $latest_query_end;
            $self->{'_sbjctStop'} = $latest_sbjct_end;
        }
        
        
        if($seqType =~ /list|array/i) {
            return ($self->{'_queryStop'}, $self->{'_sbjctStop'});
        } else {
            ## Sensitive to member name changes.
            $seqType = "_\L$seqType\E";
            return $self->{$seqType.'Stop'};
        }
    }
}

=head2 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   : L<start()|start>, L<end()|end>

=cut

sub range {
    my ($self, $seqType) = @_;
    $seqType ||= 'query';
    $seqType = 'sbjct' if $seqType eq 'hit';
    return ($self->start($seqType), $self->end($seqType));
}


=head2 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   : L<frac_conserved()|frac_conserved>, L<frac_aligned_query()|frac_aligned_query>, L<matches()|matches>, L<Bio::Search::SearchUtils::tile_hsps()|Bio::Search::SearchUtils>

=cut

sub frac_identical {
    my ($self, $seqType) = @_;
    $seqType ||= 'query';
    $seqType = 'sbjct' if $seqType eq 'hit';

    ## Sensitive to member name format.
    $seqType = lc($seqType);

    unless ($self->{'_hsps'}) {
        Bio::Search::SearchUtils::_warn_about_no_hsps($self);
        #return wantarray ? ('-','-') : '-';
        return '-';
    }

    Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps;

    my $ident = $self->matches('id');
    my $total = $self->length_aln($seqType);
    my $ratio = $ident / $total;
    my $ratio_rounded = sprintf( "%.3f", $ratio);

    # Round down iff normal rounding yields 1 (just like blast)
    $ratio_rounded = 0.999 if (($ratio_rounded == 1) && ($ratio < 1));
    return $ratio_rounded;
}


=head2 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   : L<frac_identical()|frac_identical>, L<matches()|matches>, L<Bio::Search::SearchUtils::tile_hsps()|Bio::Search::SearchUtils>

=cut

sub frac_conserved {
    my ($self, $seqType) = @_;
    $seqType ||= 'query';
    $seqType = 'sbjct' if $seqType eq 'hit';

    ## Sensitive to member name format.
    $seqType = lc($seqType);

    unless ($self->{'_hsps'}) {
        Bio::Search::SearchUtils::_warn_about_no_hsps($self);
        #return wantarray ? ('-','-') : '-';
        return '-';
    }

    Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps;

    my $consv = $self->matches('cons');
    my $total = $self->length_aln($seqType);
    my $ratio = $consv / $total;
    my $ratio_rounded = sprintf( "%.3f", $ratio);

    # Round down iff normal rounding yields 1 (just like blast)
    $ratio_rounded = 0.999 if (($ratio_rounded == 1) && ($ratio < 1));
    return $ratio_rounded;
}




=head2 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   : L<frac_aligned_hit()|frac_aligned_hit>, L<logical_length()|logical_length>, L<length_aln()|length_aln>,  L<Bio::Search::SearchUtils::tile_hsps()|Bio::Search::SearchUtils>

=cut

sub frac_aligned_query {
    my $self = shift;

    unless ($self->{'_hsps'}) {
        Bio::Search::SearchUtils::_warn_about_no_hsps($self);
        #return wantarray ? ('-','-') : '-';
        return '-';
    }

    Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps;

    my $qry_len = $self->logical_length('query');
    return undef if $qry_len == 0; # Avoid division by 0 crash
    sprintf( "%.2f", $self->length_aln('query') / $qry_len);
}



=head2 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   : L<frac_aligned_query()|frac_aligned_query>, L<matches()|matches>, , L<logical_length()|logical_length>, L<length_aln()|length_aln>,  L<Bio::Search::SearchUtils::tile_hsps()|Bio::Search::SearchUtils>

=cut

sub frac_aligned_hit {
    my $self = shift;

    unless ($self->{'_hsps'}) {
        Bio::Search::SearchUtils::_warn_about_no_hsps($self);
        #return wantarray ? ('-','-') : '-';
        return '-';
    }

    Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps;

    my $sbjct_len = $self->logical_length('sbjct');
    return undef if $sbjct_len == 0; # Avoid division by 0 crash
    sprintf( "%.2f", $self->length_aln('sbjct') / $sbjct_len);
}


## These methods are being maintained for backward compatibility. 

=head2 frac_aligned_sbjct

Same as L<frac_aligned_hit()|frac_aligned_hit>

=cut

*frac_aligned_sbjct = \&frac_aligned_hit;

=head2 num_unaligned_sbjct

Same as L<num_unaligned_hit()|num_unaligned_hit>

=cut

*num_unaligned_sbjct = \&num_unaligned_hit;


=head2 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   : L<num_unaligned_query()|num_unaligned_query>,  L<Bio::Search::SearchUtils::tile_hsps()|Bio::Search::SearchUtils>, L<frac_aligned_hit()|frac_aligned_hit>

=cut

sub num_unaligned_hit {
    my $self = shift;

    unless ($self->{'_hsps'}) {
        Bio::Search::SearchUtils::_warn_about_no_hsps($self);
        #return wantarray ? ('-','-') : '-';
        return '-';
    }

    Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps;

    my $num = $self->logical_length('sbjct') - $self->length_aln('sbjct');
    ($num < 0 ? 0 : $num );
}


=head2 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   : L<num_unaligned_hit()|num_unaligned_hit>, L<frac_aligned_query()|frac_aligned_query>,  L<Bio::Search::SearchUtils::tile_hsps()|Bio::Search::SearchUtils>

=cut

sub num_unaligned_query {
    my $self = shift;

    unless ($self->{'_hsps'}) {
        Bio::Search::SearchUtils::_warn_about_no_hsps($self);
        #return wantarray ? ('-','-') : '-';
        return '-';
    }

    Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps;

    my $num = $self->logical_length('query') - $self->length_aln('query');
    ($num < 0 ? 0 : $num );
}



=head2 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   : L<Bio::Search::HSP::BlastHSP::seq_inds()|Bio::Search::HSP::BlastHSP>

=cut

sub seq_inds {
    my ($self, $seqType, $class, $collapse) = @_;

    $seqType  ||= 'query';
    $class ||= 'identical';
    $collapse ||= 0;

    $seqType = 'sbjct' if $seqType eq 'hit';

    my (@inds, $hsp);
    foreach $hsp ($self->hsps) {
        # This will merge data for all HSPs together.
        push @inds, $hsp->seq_inds($seqType, $class);
    }
    
    # Need to remove duplicates and sort the merged positions.
    if(@inds) {
        my %tmp = map { $_, 1 } @inds;
        @inds = sort {$a <=> $b} keys %tmp;
    }

    $collapse ?  &Bio::Search::SearchUtils::collapse_nums(@inds) : @inds; 
}


=head2 strand

See documentation in L<Bio::Search::Hit::HitI::strand()|Bio::Search::Hit::HitI>

=cut

sub strand {
    my ($self, $seqType, $strnd) = @_;

    unless ($self->{'_hsps'}) {
        Bio::Search::SearchUtils::_warn_about_no_hsps($self);
        return wantarray ? ('-','-') : '-';
        #return '-';
    }

    Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps;

    $seqType ||= (wantarray ? 'list' : 'query');
    $seqType = 'sbjct' if $seqType eq 'hit';

    $seqType = lc($seqType);

    if( defined $strnd ) {
        $self->throw("Can't set strand for seqType '$seqType'. Must be 'query' or 'hit'\n") unless ($seqType eq 'sbjct' or $seqType eq 'query');

        return $self->{'_strand_'.$seqType} = $strnd;
    }

    my ($qstr, $hstr);
    # If there is only one HSP, defer this call to the solitary HSP.
    if($self->num_hsps == 1) {
        return $self->hsp->strand($seqType);
    } 
    elsif( defined $self->{'_strand_query'}) {
        # Get the data computed during hsp tiling.
        $qstr = $self->{'_strand_query'};
        $hstr = $self->{'_strand_sbjct'}
    }
    else {
        # otherwise, iterate through all HSPs collecting strand info.
        # This will return the string "-1/1" if there are HSPs on different strands.
        # NOTE: This was the pre-10/21/02 procedure which will no longer be used,
        # (unless the above elsif{} is commented out).
        my (%qstr, %hstr);
        foreach my $hsp( $self->hsps ) {
            my ( $q, $h ) = $hsp->strand();
            $qstr{ $q }++;
            $hstr{ $h }++;
        }
        $qstr = join( '/', sort keys %qstr);
        $hstr = join( '/', sort keys %hstr);
    }

    if($seqType =~ /list|array/i) {
        return ($qstr, $hstr);
    } elsif( $seqType eq 'query' ) {
        return $qstr;
    } else {
        return $hstr;
    }
}

=head2 frame

See documentation in L<Bio::Search::Hit::HitI::frame()|Bio::Search::Hit::HitI>

=cut

sub frame {
    my( $self, $frm ) = @_;

    unless ($self->{'_hsps'}) {
        Bio::Search::SearchUtils::_warn_about_no_hsps($self);
        #return wantarray ? ('-','-') : '-';
        return '-';
    }

    Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps;

    if( defined $frm ) {
        return $self->{'_frame'} = $frm;
    }

    # The check for $self->{'_frame'} is a remnant from the 'query' mode days
    # in which the sbjct object would collect data from the description line only.

    my ($frame);
    if(not defined($self->{'_frame'})) {
        $frame = $self->hsp->frame('hit');
    } else {
        $frame = $self->{'_frame'}; 
    } 
    return $frame;
}

=head2 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)


=cut

sub rank {
    my $self = shift;
    return $self->{'_rank'} = shift if @_;
    return $self->{'_rank'} || 1;
}

=head2 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

=cut

sub locus {
    my ($self,$value) = @_;
    my $previous = $self->{'_locus'};
    if( defined $value || ! defined $previous ) { 
      unless (defined $value) {
        if ($self->{'_name'} =~/(gb|emb|dbj|ref)\|(.*)\|(.*)/) {
                  $value = $previous = $3;
                } else {
          $value = $previous = '';
        }
      }
          $self->{'_locus'} = $value;
    } 
        return $previous;
}

=head2 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

=cut

sub each_accession_number {
    my ($self,$value) = @_;
    my $desc = $self->{'_description'};
    #put primary accnum on the list
    my @accnums;
    push (@accnums,$self->{'_accession'});
    if( defined $desc )  { 
      while ($desc =~ /(\b\S+\|\S*\|\S*\s?)/g) {
        my $id = $1;
        my ($acc, $version);
        if ($id =~ /(gb|emb|dbj|sp|pdb|bbs|ref|tp[gde])\|(.*)\|(.*)/) {
            ($acc, $version) = split /\./, $2; 
        } elsif ($id =~ /(pir|prf|pat|gnl)\|(.*)\|(.*)/) {
            ($acc, $version) = split /\./, $3;  
        } elsif( $id =~ /(gim|gi|bbm|bbs|lcl)\|(\d*)/) {
            $acc = $id;
        } elsif( $id =~ /(oth)\|(.*)\|(.*)\|(.*)/ ) { # discontinued...
            ($acc,$version) = ($2);
        } else {
                     #punt, not matching the db's at ftp://ftp.ncbi.nih.gov/blast/db/README
                     #Database Name                     Identifier Syntax
          #============================      ========================
          #GenBank                           gb|accession|locus
          #EMBL Data Library                 emb|accession|locus
          #DDBJ, DNA Database of Japan       dbj|accession|locus
          #NBRF PIR                          pir||entry
          #Protein Research Foundation       prf||name
          #SWISS-PROT                        sp|accession|entry name
          #Brookhaven Protein Data Bank      pdb|entry|chain
          #Patents                           pat|country|number 
          #GenInfo Backbone Id               bbs|number 
          #General database identifier           gnl|database|identifier
          #NCBI Reference Sequence           ref|accession|locus
          #Local Sequence identifier         lcl|identifier
              $acc=$id;
            }
            push(@accnums, $acc);
          }
    }  
    return @accnums;
}

=head2 tiled_hsps

See documentation in L<Bio::Search::SearchUtils::tile_hsps()|Bio::Search::SearchUtils>

=cut

sub tiled_hsps { 
    my $self = shift;
    return $self->{'_tiled_hsps'} = shift if @_;
    return $self->{'_tiled_hsps'};
}

=head2 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)


=cut

sub query_length {
    my ($self,$value) = @_;
    my $previous = $self->{'_query_length'};
    if( defined $value || ! defined $previous ) {
        $value = $previous = 0 unless defined $value;
        $self->{'_query_length'} = $value;
    }
    return $previous;
}

=head2 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
           
=cut

sub ncbi_gi {
    my ($self,$value) = @_;
    if( defined $value ) {
        $self->{'_ncbi_gi'} = $value;
    } else {
        $self->{'_ncbi_gi'} = $self->name =~ m{^gi\|(\d+)} ? $1 : '';
    } 
    return $self->{'_ncbi_gi'};
}


# sort method for HSPs

=head2 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);

=cut

sub sort_hsps {
    my ($self, $coderef) = @_;
    my @sorted_hsps;

    if ($coderef)  {
        $self->throw('sort_hsps requires a sort function passed as a subroutine reference')
            unless (ref($coderef) eq 'CODE');
    }
    else {
        $coderef = \&_default_sort_hsps;
        # throw a warning?
    }

    my @hsps = $self->hsps();
    eval {@sorted_hsps = sort $coderef @hsps };

   if ($@) {
       $self->throw("Unable to sort hsps: $@");
   }
   else {
       $self->{'_hsps'} = \@sorted_hsps;
       1;
   }
}

=head2 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   : L<found_again()|found_again>

=cut

sub iteration{
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'_psiblast_iteration'} = $value;
    }
    return $self->{'_psiblast_iteration'};
}

=head2 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   : L<iteration()|iteration>

=cut

sub found_again {
   my $self = shift;
   return $self->{'_found_again'} = shift if @_;
   return $self->{'_found_again'};
}

1;