| Bio::Phylo::Matrices::Datum - Character state sequence |
Bio::Phylo::Matrices::Datum - Character state sequence
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);
The datum object models a single observation or a sequence of observations, which can be linked to a taxon object.
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
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_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.
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).
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_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_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
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
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
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
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
validate()
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
clone()
Clones invocant.
Type : Utility method Title : clone Usage : my $clone = $object->clone; Function: Creates a copy of the invocant object. Returns : A copy of the invocant. Args : None. Comments: Cloning is currently experimental, use with caution.
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!
This object inherits from the Bio::Phylo::Taxa::TaxonLinker manpage, so the methods defined therein are also applicable to the Bio::Phylo::Matrices::Datum manpage objects.
This object inherits from the Bio::Phylo::Matrices::TypeSafeData manpage, so the methods defined therein are also applicable to the Bio::Phylo::Matrices::Datum manpage objects.
Also see the manual: the Bio::Phylo::Manual manpage and http://rutgervos.blogspot.com.
$Id: Datum.pm 1183 2009-08-02 02:07:00Z maj1 $
| Bio::Phylo::Matrices::Datum - Character state sequence |