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 Argument  : An gap_char string (optional)

=cut

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

=head2 symbol_chars

 Title   : symbol_chars
 Usage   : my @symbolchars = $aln->symbol_chars;
 Function: Returns all the seen symbols (other than gaps)
 Returns : array of characters that are the seen symbols
 Argument: boolean to include the gap/missing/match characters

=cut

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

=head1 Alignment descriptors

These read only methods describe the MSE in various ways.


=head2 consensus_string

 Title     : consensus_string
 Usage     : $str = $ali->consensus_string($threshold_percent)
 Function  : Makes a strict consensus
 Returns   : consensus string
 Argument  : Optional threshold ranging from 0 to 100.
             The consensus residue has to appear at least threshold %
             of the sequences at a given location, otherwise a '?'
             character will be placed at that location.
             (Default value = 0%)

=cut

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

=head2 consensus_iupac

 Title     : consensus_iupac
 Usage     : $str = $ali->consensus_iupac()
 Function  :

             Makes a consensus using IUPAC ambiguity codes from DNA
             and RNA. The output is in upper case except when gaps in
             a column force output to be in lower case.

             Note that if your alignment sequences contain a lot of
             IUPAC ambiquity codes you often have to manually set
             alphabet.  Bio::PrimarySeq::_guess_type thinks they
             indicate a protein sequence.

 Returns   : consensus string
 Argument  : none
 Throws    : on protein sequences


=cut

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

=head2 is_flush

 Title     : is_flush
 Usage     : if( $ali->is_flush() )
           :
           :
 Function  : Tells you whether the alignment
           : is flush, ie all of the same length
           :
           :
 Returns   : 1 or 0
 Argument  :

=cut

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

=head2 length

 Title     : length()
 Usage     : $len = $ali->length()
 Function  : Returns the maximum length of the alignment.
             To be sure the alignment is a block, use is_flush
 Returns   : integer
 Argument  :

=cut

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

=head2 maxname_length

 Title     : maxname_length
 Usage     : $ali->maxname_length()
 Function  :

             Gets the maximum length of the displayname in the
             alignment. Used in writing out various MSE formats.

 Returns   : integer