Rutger Vos > Bio-Phylo-0.55 > Bio::Phylo::Matrices::Datatype::Continuous

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Source   Latest Release: Bio-Phylo-0.58

NAME ^

Bio::Phylo::Matrices::Datatype::Continuous - Validator subclass, no serviceable parts inside

DESCRIPTION ^

The Bio::Phylo::Matrices::Datatype::* classes are used to validated data contained by Bio::Phylo::Matrices::Matrix and Bio::Phylo::Matrices::Datum objects.

METHODS ^

MUTATORS

set_lookup()

Sets the lookup table (no-op for continuous data!).

 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

ACCESSORS

get_lookup()

Gets the lookup table (no-op for continuous data!).

 Type    : Accessor
 Title   : get_lookup
 Usage   : my $lookup = $obj->get_lookup;
 Function: Returns the object's lookup hash
 Returns : A hash reference
 Args    : None

TESTS

is_valid()

Validates arguments for data validity.

 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 list of Bio::Phylo::Matrices::Datum object, and/or
           character array references, and/or character strings,
           and/or single characters

UTILITY METHODS

split()

Splits string of characters on whitespaces.

 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 array ref of characters to a space-separated string.

 Type    : Utility method
 Title   : join
 Usage   : $obj->join($arrayref)
 Function: Joins $arrayref into a string
 Returns : A string
 Args    : An array reference

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::Matrices::Datatype

This object inherits from Bio::Phylo::Matrices::Datatype, so the methods defined therein are also applicable to Bio::Phylo::Matrices::Datatype::Continuous 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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