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. 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.
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 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. 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).
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 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
Retrieves character annotations (array ref).
Type : Accessor Title : get_annotations Usage : my @anno = @{ $datum->get_annotation() }; Function: Retrieves annotations Returns : ARRAY Args : NONE
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::Matrices::DatumRole, 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.