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Manual Reference Pages  -  BIO::PHYLO::MATRICES::TYPESAFEDATA (3)

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NAME

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

CONTENTS

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 objects 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 objects 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 objects 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 objects 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 objects 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 objects 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 objects contents
 Returns : True or throws Bio::Phylo::Util::Exceptions::InvalidData
 Args    : None
 Comments: This is an abstract method, i.e. this class doesnt
           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:

<B>Rutger A VosB>, <B>Jason CaravasB>, <B>Klaas HartmannB>, <B>Mark A JensenB> and <B>Chase MillerB>, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics <B>12B>:63. <http://dx.doi.org/10.1186/1471-2105-12-63>

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perl v5.20.3 BIO::PHYLO::MATRICES::TYPESAFEDATA (3) 2014-02-08

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