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Bio/Assembly/Contig.pm  view on Meta::CPAN

=cut

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

=head2 match_char

 Title     : match_char
 Usage     : $contig->match_char('.')
 Function  : Gets/sets the match_char attribute of the alignment
 Returns   : An match_char string,
 Argument  : An match_char string (optional)

=cut

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

=head2 gap_char

 Title     : gap_char
 Usage     : $contig->gap_char('-')
 Function  : Gets/sets the gap_char attribute of the alignment
 Returns   : An gap_char string, defaults to '-'
 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 = $contig->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();
}

=head2 Alignment descriptors

These read only methods describe the MSE in various ways.


=head2 consensus_string

 Title     : consensus_string
 Usage     : $str = $contig->consensus_string($threshold_percent)
 Function  : Makes a strict consensus
 Returns   :
 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 = $contig->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( $contig->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();

Bio/Assembly/Contig.pm  view on Meta::CPAN

sub length {
    my ($self) = @_;

    $self->throw_not_implemented();
}

=head2 maxname_length

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

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

 Returns   : integer
 Argument  :

=cut

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

=head2 num_residues

 Title     : num_residues
 Usage     : $no = $contig->num_residues
 Function  : number of residues in total in the alignment
 Returns   : integer
 Argument  :
 Note      : replaces no_residues

=cut

sub num_residues {
    my ($self) = @_;

    return $self->{'_nof_residues'};
}

=head2 num_sequences

 Title     : num_sequences
 Usage     : $depth = $contig->num_sequences
 Function  : number of sequence in the sequence alignment
 Returns   : integer
 Argument  : None
 Note      : replaces no_sequences

=cut

sub num_sequences {
    my ($self) = @_;

    return scalar( keys %{ $self->{'_elem'} } );
}

=head2 percentage_identity

 Title   : percentage_identity
 Usage   : $id = $contig->percentage_identity
 Function: The function calculates the percentage identity of the alignment
 Returns : The percentage identity of the alignment (as defined by the
                             implementation)
 Argument: None

=cut

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

=head2 overall_percentage_identity

 Title   : percentage_identity
 Usage   : $id = $contig->percentage_identity
 Function: The function calculates the percentage identity of
           the conserved columns
 Returns : The percentage identity of the conserved columns
 Args    : None

=cut

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


=head2 average_percentage_identity

 Title   : average_percentage_identity
 Usage   : $id = $contig->average_percentage_identity
 Function: The function uses a fast method to calculate the average
           percentage identity of the alignment
 Returns : The average percentage identity of the alignment
 Args    : None

=cut

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

=head2 Alignment positions

Methods to map a sequence position into an alignment column and back.
column_from_residue_number() does the former. The latter is really a
property of the sequence object and can done using
L<Bio::LocatableSeq::location_from_column>:

    # select somehow a sequence from the alignment, e.g.
    my $seq = $contig->get_seq_by_pos(1);
    #$loc is undef or Bio::LocationI object
    my $loc = $seq->location_from_column(5);


=head2 column_from_residue_number

 Title   : column_from_residue_number
 Usage   : $col = $contig->column_from_residue_number( $seqname, $resnumber)
 Function:

           This function gives the position in the alignment
           (i.e. column number) of the given residue number in the
           sequence with the given name. For example, for the
           alignment

           Seq1/91-97 AC..DEF.GH
           Seq2/24-30 ACGG.RTY..
           Seq3/43-51 AC.DDEFGHI

           column_from_residue_number( "Seq1", 94 ) returns 5.
           column_from_residue_number( "Seq2", 25 ) returns 2.
           column_from_residue_number( "Seq3", 50 ) returns 9.

           An exception is thrown if the residue number would lie
           outside the length of the aligment
           (e.g. column_from_residue_number( "Seq2", 22 )

      Note: If the the parent sequence is represented by more than
      one alignment sequence and the residue number is present in
      them, this method finds only the first one.

 Returns : A column number for the position in the alignment of the
           given residue in the given sequence (1 = first column)
 Args    : A sequence id/name (not a name/start-end)
           A residue number in the whole sequence (not just that
           segment of it in the alignment)

=cut

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

=head2 Sequence names

Methods to manipulate the display name. The default name based on the