Rutger Vos > Bio-Phylo-0.56 > Bio::Phylo::Matrices::Datatype::Mixed

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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

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