NAME

Bio::Phylo::Matrices::Datum - Character state sequence

SYNOPSIS

use Bio::Phylo::Factory;
my $fac = Bio::Phylo::Factory->new;

# instantiating a datum object...
my $datum = $fac->create_datum(
   -name   => 'Tooth comb size,
   -type   => 'STANDARD',
   -desc   => 'number of teeth in lower jaw comb',
   -pos    => 1,
   -weight => 2,
   -char   => [ 6 ],
);

# ...and linking it to a taxon object
my $taxon = $fac->create_taxon(
    -name => 'Lemur_catta'
);
$datum->set_taxon( $taxon );

# instantiating a matrix...
my $matrix = $fac->create_matrix;

# ...and insert datum in matrix
$matrix->insert($datum);

DESCRIPTION

The datum object models a single observation or a sequence of observations, which can be linked to a taxon object. This package contains the getters and setters that alter the internal state of the datum object. Additional (stateless) behaviours are defined in the Bio::Phylo::Matrices::DatumRole package.

METHODS

MUTATORS

set_weight()

Sets invocant weight.

Type    : Mutator
Title   : set_weight
Usage   : $datum->set_weight($weight);
Function: Assigns a datum's weight.
Returns : Modified object.
Args    : The $weight argument must be a
          number in any of Perl's number
          formats.

set_position()

Set invocant starting position.

Type    : Mutator
Title   : set_position
Usage   : $datum->set_position($pos);
Function: Assigns a datum's position.
Returns : Modified object.
Args    : $pos must be an integer.

set_annotation()

Sets single annotation.

Type    : Mutator
Title   : set_annotation
Usage   : $datum->set_annotation(
              -char       => 1,
              -annotation => { -codonpos => 1 }
          );
Function: Assigns an annotation to a
          character in the datum.
Returns : Modified object.
Args    : Required: -char       => $int
          Optional: -annotation => $hashref
Comments: Use this method to annotate
          a single character. To annotate
          multiple characters, use
          'set_annotations' (see below).

set_annotations()

Sets list of annotations.

Type    : Mutator
Title   : set_annotations
Usage   : $datum->set_annotations(
              { '-codonpos' => 1 },
              { '-codonpos' => 2 },
              { '-codonpos' => 3 },
          );
Function: Assign annotations to
          characters in the datum.
Returns : Modified object.
Args    : Hash references, where
          position in the argument
          list matches that of the
          specified characters in
          the character list. If no
          argument given, annotations
          are reset.
Comments: Use this method to annotate
          multiple characters. To
          annotate a single character,
          use 'set_annotation' (see
          above).

ACCESSORS

get_weight()

Gets invocant weight.

Type    : Accessor
Title   : get_weight
Usage   : my $weight = $datum->get_weight;
Function: Retrieves a datum's weight.
Returns : FLOAT
Args    : NONE

get_position()

Gets invocant starting position.

Type    : Accessor
Title   : get_position
Usage   : my $pos = $datum->get_position;
Function: Retrieves a datum's position.
Returns : a SCALAR integer.
Args    : NONE

get_annotation()

Retrieves character annotation (hashref).

Type    : Accessor
Title   : get_annotation
Usage   : $datum->get_annotation(
              '-char' => 1,
              '-key'  => '-codonpos',
          );
Function: Retrieves an annotation to
          a character in the datum.
Returns : SCALAR or HASH
Args    : Optional: -char => $int
          Optional: -key => $key

get_annotations()

Retrieves character annotations (array ref).

Type    : Accessor
Title   : get_annotations
Usage   : my @anno = @{ $datum->get_annotation() };
Function: Retrieves annotations
Returns : ARRAY
Args    : NONE

SEE ALSO

There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.

Bio::Phylo::Matrices::DatumRole

This object inherits from Bio::Phylo::Matrices::DatumRole, so the methods defined therein are also applicable to Bio::Phylo::Matrices::Datum objects.

Bio::Phylo::Manual

Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com.

CITATION

If you use Bio::Phylo in published research, please cite it:

Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12:63. http://dx.doi.org/10.1186/1471-2105-12-63