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Bio::Phylo::Matrices::TypeSafeData(3) User Contributed Perl Documentation Bio::Phylo::Matrices::TypeSafeData(3)

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

 # No direct usage

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.

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)
    

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
    

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
    

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
    

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>.

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>

2017-10-30 perl v5.32.1

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