NAME

Bio::Phylo::Matrices::Datatype - Validator of character state data

SYNOPSIS

 # No direct usage

DESCRIPTION

This is a superclass for objects that validate character data. Objects that inherit from this class (typically those in the Bio::Phylo::Matrices::Datatype::* namespace) can check strings and arrays of character data for invalid symbols, and split and join strings and arrays in a way appropriate for the type (on whitespace for continuous data, on single characters for categorical data). Bio::Phylo::Matrices::Matrix objects and Bio::Phylo::Matrices::Datum internally delegate validation of their contents to these datatype objects; there is no normal usage in which you'd have to deal with datatype objects directly.

METHODS

CONSTRUCTOR

new()

Datatype constructor.

 Type    : Constructor
 Title   : new
 Usage   : No direct usage, is called by TypeSafeData classes;
 Function: Instantiates a Datatype object
 Returns : a Bio::Phylo::Matrices::Datatype child class
 Args    : $type (optional, one of continuous, custom, dna,
           mixed, protein, restriction, rna, standard)

MUTATORS

set_lookup()

Sets state lookup table.

 Type    : Mutator
 Title   : set_lookup
 Usage   : $obj->set_lookup($hashref);
 Function: Sets the state lookup table.
 Returns : Modified object.
 Args    : Argument must be a hash
           reference that maps allowed
           single character symbols
           (including ambiguity symbols)
           onto the equivalent set of
           non-ambiguous symbols

set_missing()

Sets missing data symbol.

 Type    : Mutator
 Title   : set_missing
 Usage   : $obj->set_missing('?');
 Function: Sets the symbol for missing data
 Returns : Modified object.
 Args    : Argument must be a single
           character, default is '?'

set_gap()

Sets gap symbol.

 Type    : Mutator
 Title   : set_gap
 Usage   : $obj->set_gap('-');
 Function: Sets the symbol for gaps
 Returns : Modified object.
 Args    : Argument must be a single
           character, default is '-'

set_metas_for_states()

Assigns all metadata annotations for all state symbols

 Type    : Mutator
 Title   : set_metas_for_states
 Usage   : $obj->set_metas_for_states({ $state => [ $m1, $m2 ] });
 Function: Assigns all metadata annotations for all state symbols
 Returns : Modified object.
 Args    : A hash reference of state symbols with metadata arrays

add_meta_for_state()

Adds a metadata annotation for a state symbol

 Type    : Mutator
 Title   : add_meta_for_state
 Usage   : $obj->add_meta_for_state($meta,$state);
 Function: Adds a metadata annotation for a state symbol
 Returns : Modified object.
 Args    : A Bio::Phylo::NeXML::Meta object and a state symbol

remove_meta_for_state()

Removes a metadata annotation for a state symbol

 Type    : Mutator
 Title   : remove_meta_for_state
 Usage   : $obj->remove_meta_for_state($meta,$state);
 Function: Removes a metadata annotation for a state symbol
 Returns : Modified object.
 Args    : A Bio::Phylo::NeXML::Meta object and a state symbol

ACCESSORS

get_type()

Gets data type as string.

 Type    : Accessor
 Title   : get_type
 Usage   : my $type = $obj->get_type;
 Function: Returns the object's datatype
 Returns : A string
 Args    : None

get_ids_for_special_symbols()

Gets state-to-id mapping for missing and gap symbols

 Type    : Accessor
 Title   : get_ids_for_special_symbols
 Usage   : my %ids = %{ $obj->get_ids_for_special_symbols };
 Function: Returns state-to-id mapping
 Returns : A hash reference, keyed on symbol, with UID values
 Args    : Optional, a boolean:
           true  => prefix state ids with 's'
           false => keep ids numerical

get_ids_for_states()

Gets state-to-id mapping

 Type    : Accessor
 Title   : get_ids_for_states
 Usage   : my %ids = %{ $obj->get_ids_for_states };
 Function: Returns state-to-id mapping
 Returns : A hash reference, keyed on symbol, with UID values
 Args    : Optional, a boolean:
           true  => prefix state ids with 's'
           false => keep ids numerical
 Note    : This returns a mapping to alphanumeric states; special
           symbols (for missing data and gaps) are handled separately

get_states_for_symbol()

Gets set of fundamental states for an ambiguity symbol

 Type    : Accessor
 Title   : get_states_for_symbol
 Usage   : my @states = @{ $obj->get_states_for_symbol('N') };
 Function: Returns the set of states for an ambiguity symbol
 Returns : An array ref of symbols
 Args    : An ambiguity symbol
 Comments: If supplied argument is a fundamental state, an array
           ref with just that state is returned, e.g. 'A' returns
           ['A'] for DNA and RNA

get_symbol_for_states()

Gets ambiguity symbol for a set of states

 Type    : Accessor
 Title   : get_symbol_for_states
 Usage   : my $state = $obj->get_symbol_for_states('A','C');
 Function: Returns the ambiguity symbol for a set of states
 Returns : A symbol (SCALAR)
 Args    : A set of symbols
 Comments: If no symbol exists in the lookup
           table for the given set of states,
           a new - numerical - one is created

get_lookup()

Gets state lookup table.

 Type    : Accessor
 Title   : get_lookup
 Usage   : my $lookup = $obj->get_lookup;
 Function: Returns the object's lookup hash
 Returns : A hash reference
 Args    : None

get_missing()

Gets missing data symbol.

 Type    : Accessor
 Title   : get_missing
 Usage   : my $missing = $obj->get_missing;
 Function: Returns the object's missing data symbol
 Returns : A string
 Args    : None

get_gap()

Gets gap symbol.

 Type    : Accessor
 Title   : get_gap
 Usage   : my $gap = $obj->get_gap;
 Function: Returns the object's gap symbol
 Returns : A string
 Args    : None

get_meta_for_state()

Gets metadata annotations (if any) for the provided state symbol

 Type    : Accessor
 Title   : get_meta_for_state
 Usage   : my @meta = @{ $obj->get_meta_for_state };
 Function: Gets metadata annotations for a state symbol
 Returns : An array reference of Bio::Phylo::NeXML::Meta objects
 Args    : A state symbol

get_metas_for_states()

Gets metadata annotations (if any) for all state symbols

 Type    : Accessor
 Title   : get_metas_for_states
 Usage   : my @meta = @{ $obj->get_metas_for_states };
 Function: Gets metadata annotations for state symbols
 Returns : An array reference of Bio::Phylo::NeXML::Meta objects
 Args    : None

TESTS

is_ambiguous()

Tests whether the supplied state symbol represents an ambiguous (polymorphic or uncertain) state. For example, for the most commonly-used alphabet for DNA states, the symbol 'N' represents complete uncertainty, the actual state could be any of 'A', 'C', 'G' or 'T', and so this method would return a true value.

 Type    : Test
 Title   : is_ambiguous
 Usage   : if ( $obj->is_ambiguous('N') ) {
              # do something
           }
 Function: Returns true if argument is an ambiguous state symbol
 Returns : BOOLEAN
 Args    : A state symbol

is_valid()

Validates argument.

 Type    : Test
 Title   : is_valid
 Usage   : if ( $obj->is_valid($datum) ) {
              # do something
           }
 Function: Returns true if $datum only contains valid characters
 Returns : BOOLEAN
 Args    : A Bio::Phylo::Matrices::Datum object

is_same()

Compares data type objects.

 Type    : Test
 Title   : is_same
 Usage   : if ( $obj->is_same($obj1) ) {
              # do something
           }
 Function: Returns true if $obj1 contains the same validation rules
 Returns : BOOLEAN
 Args    : A Bio::Phylo::Matrices::Datatype::* object

UTILITY METHODS

split()

Splits argument string of characters following appropriate rules.

 Type    : Utility method
 Title   : split
 Usage   : $obj->split($string)
 Function: Splits $string into characters
 Returns : An array reference of characters
 Args    : A string

join()

Joins argument array ref of characters following appropriate rules.

 Type    : Utility method
 Title   : join
 Usage   : $obj->join($arrayref)
 Function: Joins $arrayref into a string
 Returns : A string
 Args    : An array reference

SERIALIZERS

to_xml()

Writes data type definitions to xml

 Type    : Serializer
 Title   : to_xml
 Usage   : my $xml = $obj->to_xml
 Function: Writes data type definitions to xml
 Returns : An xml string representation of data type definition
 Args    : None

to_dom()

Analog to to_xml.

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

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>