NAME

Bio::Phylo::Matrices::DatumRole - Extra behaviours for a 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.

METHODS

CONSTRUCTOR

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,

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

MUTATORS

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
           PROTEIN), integers (STANDARD) or any of perl's
           decimal formats (CONTINUOUS). The $char can be:
               * a single character;
               * a string of characters;
               * an array reference of characters;
               * an array of characters;
 Comments: Note that on assigning characters to a datum,
           previously set annotations are removed.

ACCESSORS

get_matrix()

Gets the matrix (if any) this datum belongs to

 Type    : Accessor
 Title   : get_matrix
 Usage   : my $matrix = $datum->get_matrix;
 Function: Retrieves the matrix the datum belongs to
 Returns : Bio::Phylo::Matrices::Matrix
 Args    : NONE

get_char()

Gets characters.

 Type    : Accessor
 Title   : get_char
 Usage   : my $char = $datum->get_char;
 Function: Retrieves a datum's character value.
 Returns : In scalar context, returns a single
           character, or a string of characters
           (e.g. a DNA sequence, or a space
           delimited series of continuous characters).
           In list context, returns a list of characters
           (of zero or more characters).
 Args    : NONE

get_unaligned_char()

Gets unaligned characters, i.e. without gap or missing symbols

 Type    : Accessor
 Title   : get_unaligned_char
 Usage   : my $char = $datum->get_unaligned_char;
 Function: Retrieves a datum's unaligned character sequence
 Returns : In scalar context, returns a single
           character, or a string of characters
           (e.g. a DNA sequence, or a space
           delimited series of continuous characters).
           In list context, returns a list of characters
           (of zero or more characters).
 Args    : NONE

get_length()

Gets invocant number of characters.

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

get_by_index()

Gets state at argument index.

 Type    : Accessor
 Title   : get_by_index
 Usage   : my $val = $datum->get_by_index($i);
 Function: Retrieves state at index $i.
 Returns : a character state.
 Args    : INT

get_index_of()

Returns the index of the first occurrence of the state observation in the datum or undef if the datum doesn't contain the argument

 Type    : Generic query
 Title   : get_index_of
 Usage   : my $i = $datum->get_index_of($state)
 Function: Returns the index of the first occurrence of the 
           state observation in the datum or undef if the datum 
                   doesn't contain the argument
 Returns : An index or undef
 Args    : A contained object

TESTS

can_contain()

Tests if invocant can contain argument.

 Type    : Test
 Title   : can_contain
 Usage   : &do_something if $datum->can_contain( @args );
 Function: Tests if $datum can contain @args
 Returns : BOOLEAN
 Args    : One or more arguments as can be provided to set_char

CALCULATIONS

calc_state_counts()

Calculates occurrences of states.

 Type    : Calculation
 Title   : calc_state_counts
 Usage   : my %counts = %{ $datum->calc_state_counts };
 Function: Calculates occurrences of states.
 Returns : Hashref: keys are states, values are counts
 Args    : Optional - one or more states to focus on

calc_distance()

Calculates the distance between the invocant and argument

 Type    : Calculation
 Title   : calc_distance
 Usage   : my $dist = $datum1->calc_distance($datum2);
 Function: Calculates pairwise distance
 Returns : A number, the distance per site
 Args    : Another datum to calculate the distance to
 Comments: Assumes the sequences are aligned. Calculates
           substitutions / total non-missing and non-gapped sites.

calc_state_frequencies()

Calculates the frequencies of the states observed in the matrix.

 Type    : Calculation
 Title   : calc_state_frequencies
 Usage   : my %freq = %{ $object->calc_state_frequencies() };
 Function: Calculates state frequencies
 Returns : A hash, keys are state symbols, values are frequencies
 Args    : Optional:
           # if true, counts missing (usually the '?' symbol) as a state
           # in the final tallies. Otherwise, missing states are ignored
           -missing => 1
           # if true, counts gaps (usually the '-' symbol) as a state
           # in the final tallies. Otherwise, gap states are ignored
           -gap => 1
 Comments: Throws exception if matrix holds continuous values

METHODS

reverse()

Reverses contents.

 Type    : Method
 Title   : reverse
 Usage   : $datum->reverse;
 Function: Reverses a datum's contained characters
 Returns : Returns modified $datum
 Args    : NONE

concat()

Appends argument to invocant.

 Type    : Method
 Title   : reverse
 Usage   : $datum->concat($datum1);
 Function: Appends $datum1 to $datum
 Returns : Returns modified $datum
 Args    : NONE

consense()

Creates consensus sequence out of arguments

 Type    : Method
 Title   : consense
 Usage   : my @chars = $datum->consense($datum1,...);
 Function: Creates consensus sequence out of arguments
 Returns : Returns @chars or $seq
 Args    : NONE

to_xml()

Serializes datum to nexml format.

 Type    : Format convertor
 Title   : to_xml
 Usage   : my $xml = $datum->to_xml;
 Function: Converts datum object into a nexml element structure.
 Returns : Nexml block (SCALAR).
 Args    : -chars   => [] # optional, an array ref of character IDs
           -states  => {} # optional, a hash ref of state IDs
           -symbols => {} # optional, a hash ref of symbols
           -special => {} # optional, a hash ref of special symbol IDs

to_dom()

Analog to to_xml.

 Type    : Serializer
 Title   : to_dom
 Usage   : $datum->to_dom
 Function: Generates a DOM subtree from the invocant
           and its contained objects
 Returns : an XML::LibXML::Element object
 Args    : none

copy_atts()

 Not implemented!

complement()

 Not implemented!

slice()

 Not implemented!

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>