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