Bio::Phylo::Matrices::DatumRole - Extra behaviours for a 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.
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,
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
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.
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
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 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
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
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 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
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
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
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
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
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.
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
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
Not implemented!
There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.
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 and http://rutgervos.blogspot.com.
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
To install Bio::Phylo, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Phylo
CPAN shell
perl -MCPAN -e shell install Bio::Phylo
For more information on module installation, please visit the detailed CPAN module installation guide.