NAME

Bio::Phylo::Matrices::Datatype - Superclass for objects that validate character 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 (i.e. on whitespace for continuous data, on single characters for categorical data). The datatype objects are used by Bio::Phylo::Matrices::Matrix objects and Bio::Phylo::Matrices::Datum objects in an arrangement akin to the Delegation design pattern (e.g. see http://www.c2.com/cgi/wiki?DelegationPattern).

METHODS

CONSTRUCTOR

new()

Datatype constructor.

 Type    : Constructor
 Title   : new
 Usage   : No direct usage, is called by TypeSafaData 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 '-'

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_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

TESTS

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

REVISION

 $Id: Datatype.pm 4265 2007-07-20 14:14:44Z rvosa $

CPAN RT