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Bio/Search/HSP/HMMERHSP.pm  view on Meta::CPAN

                   'hit'   = num gaps in hit seq
                   'total' = num gaps in whole alignment 
                   default = 'total' 
            arg 2: [optional] integer gap value to set for the type requested

=cut

=head2 query_string

 Title   : query_string
 Usage   : my $qseq = $hsp->query_string;
 Function: Retrieves the query sequence of this HSP as a string
 Returns : string
 Args    : [optional] string to set for query sequence


=cut

=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    : [optional] string to set for hit sequence


=cut


=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    : [optional] string to set for homology sequence

=cut

=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     : arg 1: 'query' = length of query seq (without gaps)
                   'hit'   = length of hit seq (without gaps)
                   'total' = length of alignment (with gaps)
                   default = 'total' 
            arg 2: [optional] integer length value to set for specific type

=cut

=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


=head2 frame

 Title   : frame
 Usage   : my ($qframe, $hframe) = $hsp->frame('list',$queryframe,$subjectframe)
 Function: Set the Frame for both query and subject and insure that
           they agree.
           This overrides the frame() method implementation in
           FeaturePair.
 Returns : array of query and subject frame if return type wants an array
           or query frame if defined or subject frame if not defined
 Args    : 'hit' or 'subject' or 'sbjct' to retrieve the frame of the subject (default)
           'query' to retrieve the query frame 
           'list' or 'array' to retrieve both query and hit frames together
 Note    : Frames are stored in the GFF way (0-2) not 1-3
           as they are in BLAST (negative frames are deduced by checking
                                 the strand of the query or hit)

=cut

=head2 get_aln

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

=cut

sub get_aln {
    my ($self) = shift;
    $self->warn("Inappropriate to build a Bio::SimpleAlign from a HMMER HSP object");
    return;
}

=head2 num_conserved

 Title   : num_conserved
 Usage   : $obj->num_conserved($newval)
 Function: returns the number of conserved residues in the alignment
 Returns : inetger
 Args    : integer (optional)


=cut

=head2 num_identical

 Title   : num_identical
 Usage   : $obj->num_identical($newval)
 Function: returns the number of identical residues in the alignment
 Returns : integer
 Args    : integer (optional)