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sub query_string{
   my ($self) = @_;
   $self->throw_not_implemented;
}

=head2 hit_string

 Title   : hit_string
 Usage   : my $hseq = $hsp->hit_string;
 Function: Retrieves the hit sequence of this HSP as a string
 Returns : string
 Args    : none


=cut

sub hit_string{
   my ($self) = @_;
   $self->throw_not_implemented;
}

=head2 homology_string

 Title   : homology_string
 Usage   : my $homo_string = $hsp->homology_string;
 Function: Retrieves the homology sequence for this HSP as a string.
         : The homology sequence is the string of symbols in between the 
         : query and hit sequences in the alignment indicating the degree
         : of conservation (e.g., identical, similar, not similar).
 Returns : string
 Args    : none

=cut

sub homology_string{
   my ($self) = @_;
   $self->throw_not_implemented;
}

=head2 length

 Title    : length
 Usage    : my $len = $hsp->length( ['query'|'hit'|'total'] );
 Function : Returns the length of the query or hit in the alignment (without gaps) 
            or the aggregate length of the HSP (including gaps;
            this may be greater than either hit or query )
 Returns  : integer
 Args     : 'query' = length of query seq (without gaps)
            'hit'   = length of hit seq (without gaps)
            'total' = length of alignment (with gaps)
            default = 'total' 
 Args    : none

=cut

sub length{
    shift->throw_not_implemented();
}

=head2 percent_identity

 Title   : percent_identity
 Usage   : my $percentid = $hsp->percent_identity()
 Function: Returns the calculated percent identity for an HSP
 Returns : floating point between 0 and 100 
 Args    : none


=cut

sub percent_identity{
   my ($self) = @_;
   return $self->frac_identical('hsp') * 100;   
}

=head2 get_aln

 Title   : get_aln
 Usage   : my $aln = $hsp->get_aln
 Function: Returns a Bio::SimpleAlign representing the HSP alignment
 Returns : Bio::SimpleAlign
 Args    : none

=cut

sub get_aln {
   my ($self) = @_;
   $self->throw_not_implemented;
}


=head2 seq_inds

 Title   : seq_inds
 Purpose   : Get a list of residue positions (indices) for all identical 
           : or conserved residues in the query or sbjct sequence.
 Example   : @s_ind = $hsp->seq_inds('query', 'identical');
           : @h_ind = $hsp->seq_inds('hit', 'conserved');
           : @h_ind = $hsp->seq_inds('hit', 'conserved', 1);
 Returns   : List of integers 
           : May include ranges if collapse is true.
 Argument  : seq_type  = 'query' or 'hit' or 'sbjct'  (default = query)
              ('sbjct' is synonymous with 'hit') 
             class     = 'identical' or 'conserved' or 'nomatch' or 'gap'
                          (default = identical)
                          (can be shortened to 'id' or 'cons')

             collapse  = boolean, if true, 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.
 Comments  : 

See Also   : L<Bio::Search::BlastUtils::collapse_nums()|Bio::Search::BlastUtils>, L<Bio::Search::Hit::HitI::seq_inds()|Bio::Search::Hit::HitI>

=cut

sub seq_inds {
    shift->throw_not_implemented();
}

=head2 Inherited from L<Bio::SeqFeature::SimilarityPair>

These methods come from L<Bio::SeqFeature::SimilarityPair>

=head2 query

 Title   : query
 Usage   : my $query = $hsp->query
 Function: Returns a SeqFeature representing the query in the HSP