view release on metacpan or  search on metacpan

lib/Bio/Phylo/Matrices/DatumRole.pm  view on Meta::CPAN

=item new()

Datum object constructor.

 Type    : Constructor
 Title   : new
 Usage   : my $datum = Bio::Phylo::Matrices::Datum->new;
 Function: Instantiates a Bio::Phylo::Matrices::Datum
           object.
 Returns : A Bio::Phylo::Matrices::Datum object.
 Args    : None required. Optional:
           -taxon  => $taxon,
           -weight => 0.234,
           -type   => DNA,           
           -pos    => 2,

=cut

    sub new : Constructor {

        # could be child class
        my $class = shift;

        # notify user
        $logger->info("constructor called for '$class'");
        if ( not $LOADED_WRAPPERS ) {
            eval do { local $/; <DATA> };
            die $@ if $@;
            $LOADED_WRAPPERS++;
        }

        # go up inheritance tree, eventually get an ID
        my $self = $class->SUPER::new(
            @_,
            '-listener' => \&_update_characters,
        );
        return $self;
    }

=item new_from_bioperl()

Datum constructor from Bio::Seq argument.

 Type    : Constructor
 Title   : new_from_bioperl
 Usage   : my $datum = 
           Bio::Phylo::Matrices::Datum->new_from_bioperl($seq);
 Function: Instantiates a 
           Bio::Phylo::Matrices::Datum object.
 Returns : A Bio::Phylo::Matrices::Datum object.
 Args    : A Bio::Seq (or similar) object

=cut

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

        # want $seq type-check here? Allowable: is-a Bio::PrimarySeq,
        #  Bio::LocatableSeq /maj
        my $type = $seq->alphabet || $seq->_guess_alphabet || 'dna';
        my $self = $class->new( '-type' => $type, @args );

        # copy seq string
        my $seqstring = $seq->seq;
        if ( $seqstring and $seqstring =~ /\S/ ) {
            eval { $self->set_char($seqstring) };
            if (
                $@
                and looks_like_instance(
                    $@, 'Bio::Phylo::Util::Exceptions::InvalidData'
                )
              )
            {
                $logger->error(
"\nAn exception of type Bio::Phylo::Util::Exceptions::InvalidData was caught\n\n"
                      . $@->description
                      . "\n\nThe BioPerl sequence object contains invalid data ($seqstring)\n"
                      . "I cannot store this string, I will continue instantiating an empty object.\n"
                      . "---------------------------------- STACK ----------------------------------\n"
                      . $@->trace->as_string
                      . "\n--------------------------------------------------------------------------"
                );
            }
        }

        # copy name
        my $name = $seq->display_id;
        $self->set_name($name) if defined $name;

        # copy desc
        my $desc = $seq->desc;
        $self->set_desc($desc) if defined $desc;

        # only Bio::LocatableSeq objs have these fields...
        for my $field (qw(start end strand)) {
            $self->$field( $seq->$field ) if $seq->can($field);
        }
        return $self;
    }

=back

=head2 MUTATORS

=over

=item set_char()

Sets character state(s)

 Type    : Mutator
 Title   : set_char
 Usage   : $datum->set_char($char);
 Function: Assigns a datum's character value.
 Returns : Modified object.
 Args    : The $char argument is checked against
           the allowed ranges for the various
           character types: IUPAC nucleotide (for
           types of DNA|RNA|NUCLEOTIDE), IUPAC
           single letter amino acid codes (for type