Rutger Vos > Bio-Phylo > Bio::Phylo::Matrices::TypeSafeData

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NAME ^

Bio::Phylo::Matrices::TypeSafeData - Superclass for objects that contain character data

SYNOPSIS ^

 # No direct usage

DESCRIPTION ^

This is a superclass for objects holding character data. Objects that inherit from this class (typically matrices and datum objects) yield functionality to handle datatype objects and use them to validate data such as DNA sequences, continuous data etc.

METHODS ^

CONSTRUCTOR

new()

TypeSafeData constructor.

 Type    : Constructor
 Title   : new
 Usage   : No direct usage, is called by child class;
 Function: Instantiates a Bio::Phylo::Matrices::TypeSafeData
 Returns : a Bio::Phylo::Matrices::TypeSafeData child class
 Args    : -type        => (data type - required)
           Optional:
           -missing     => (the symbol for missing data)
           -gap         => (the symbol for gaps)
           -lookup      => (a character state lookup hash)
           -type_object => (a datatype object)

MUTATORS

set_type()

Set data type.

 Type    : Mutator
 Title   : set_type
 Usage   : $obj->set_type($type);
 Function: Sets the object's datatype.
 Returns : Modified object.
 Args    : Argument must be a string, one of
           continuous, custom, dna, mixed,
           protein, restriction, rna, standard
set_missing()

Set 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()

Set gap data 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_lookup()

Set ambiguity lookup table.

 Type    : Mutator
 Title   : set_lookup
 Usage   : $obj->set_gap($hashref);
 Function: Sets the symbol for gaps
 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_type_object()

Set data type object.

 Type    : Mutator
 Title   : set_type_object
 Usage   : $obj->set_gap($obj);
 Function: Sets the datatype object
 Returns : Modified object.
 Args    : Argument must be a subclass
           of Bio::Phylo::Matrices::Datatype

ACCESSORS

get_type()

Get data type.

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

Get 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()

Get 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_lookup()

Get ambiguity 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_type_object()

Get data type object.

 Type    : Accessor
 Title   : get_type_object
 Usage   : my $obj = $obj->get_type_object;
 Function: Returns the object's linked datatype object
 Returns : A subclass of Bio::Phylo::Matrices::Datatype
 Args    : None

INTERFACE METHODS

validate()

Validates the object's contents

 Type    : Interface method
 Title   : validate
 Usage   : $obj->validate
 Function: Validates the object's contents
 Returns : True or throws Bio::Phylo::Util::Exceptions::InvalidData
 Args    : None
 Comments: This is an abstract method, i.e. this class doesn't
           implement the method, child classes have to

SEE ALSO ^

There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.

Bio::Phylo::Listable

This object inherits from Bio::Phylo::Listable, so the methods defined therein are also applicable to Bio::Phylo::Matrices::TypeSafeData objects.

Bio::Phylo::Manual

Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com.

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

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