Bio::Phylo::Matrices::Datatype::Mixed(3)

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>