Bio::Phylo::Matrices::Datum - The character state sequence object.
use Bio::Phylo::Matrices::Matrix;
use Bio::Phylo::Matrices::Datum;
use Bio::Phylo::Taxa::Taxon;
# instantiating a datum object...
my $datum = Bio::Phylo::Matrices::Datum->new(
-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 = Bio::Phylo::Taxa::Taxon->new(
-name => 'Lemur_catta'
);
$datum->set_taxon( $taxon );
# instantiating a matrix...
my $matrix = Bio::Phylo::Matrices::Matrix->new;
# ...and insert datum in matrix
$matrix->insert($datum);
The datum object models a single observation or a sequence of observations, which can be linked to a taxon object.
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,
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.
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.
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.
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).
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.
Comments: Use this method to annotate
multiple characters. To
annotate a single character,
use 'set_annotation' (see
above).
Gets invocant weight.
Type : Accessor Title : get_weight Usage : my $weight = $datum->get_weight; Function: Retrieves a datum's weight. Returns : FLOAT Args : NONE
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
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
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
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
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
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
Reverses contents.
Type : Method Title : reverse Usage : $datum->reverse; Function: Reverses a datum's contained characters Returns : Returns modified $datum Args : NONE
Appends argument to invocant.
Type : Method Title : reverse Usage : $datum->concat($datum1); Function: Appends $datum1 to $datum Returns : Returns modified $datum Args : NONE
Validates invocant data contents.
Type : Method Title : validate Usage : $datum->validate; Function: Validates character data contained by $datum Returns : True or throws Bio::Phylo::Util::Exceptions::InvalidData Args : NONE
Not implemented!
Not implemented!
Not implemented!
This object inherits from Bio::Phylo::Taxa::TaxonLinker, so the methods defined therein are also applicable to Bio::Phylo::Matrices::Datum objects.
This object inherits from Bio::Phylo::Matrices::TypeSafeData, so the methods defined therein are also applicable to Bio::Phylo::Matrices::Datum objects.
Also see the manual: Bio::Phylo::Manual.
$Id: Datum.pm 4265 2007-07-20 14:14:44Z rvosa $
