Bio::Phylo::Matrices::Datatype::Mixed - Validator subclass,

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 the Bio::Phylo::Matrices::Matrix manpage and the Bio::Phylo::Matrices::Datum manpage 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

the Bio::Phylo::Matrices::Datatype manpage

This object inherits from the Bio::Phylo::Matrices::Datatype manpage, so the methods defined therein are also applicable to the Bio::Phylo::Matrices::Datatype::Mixed manpage objects.

the Bio::Phylo::Manual manpage

Also see the manual: the Bio::Phylo::Manual manpage and http://rutgervos.blogspot.com.

REVISION

 $Id: Mixed.pm 844 2009-03-05 00:07:26Z rvos $
 Bio::Phylo::Matrices::Datatype::Mixed - Validator subclass,