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Bio::Phylo::Matrices::UserSContributed PeBio::Phylo::Matrices::TypeSafeData(3)

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>

perl v5.32.1			  2017-10Bio::Phylo::Matrices::TypeSafeData(3)

NAME | SYNOPSIS | DESCRIPTION | METHODS | SEE ALSO | CITATION

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