NAME

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

DESCRIPTION

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

METHODS

MUTATORS

set_missing()

Sets the symbol for missing data.

            

              
              
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()

Sets the symbol for gaps.

            

              
              
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 '-'
            
          

ACCESSORS

get_missing()

Returns the object's 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()

Returns the object's 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_type()

Returns the object's datatype as string.

            

              
              
Type    : Accessor
Title   : get_type
Usage   : my $type = $obj->get_type;
Function: Returns the object's datatype
Returns : A string
Args    : None
            
          

get_type_for_site()

Returns type object for site number.

            

              
              
Type    : Accessor
Title   : get_type_for_site
Usage   : my $type = $obj->get_type_for_site(1);
Function: Returns data type object for site
Returns : A Bio::Phylo::Matrices::Datatype object
Args    : None
            
          

TESTS

is_same()

Compares data type objects.

            

              
              
Type    : Test
Title   : is_same
Usage   : if ( $obj->is_same($obj1) ) {
             # do something
          }
Function: Returns true if $obj1 contains the same validation rules
Returns : BOOLEAN
Args    : A Bio::Phylo::Matrices::Datatype::* object
            
          

is_valid()

Returns true if argument only contains valid characters

            

              
              
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 Bio::Phylo::Matrices::Datum object
            
          

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::Mixed 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