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Man Pages


Manual Reference Pages  -  BIO::PHYLO::MATRICES::DATATYPE::MIXED (3)

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NAME

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

CONTENTS

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 objects 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 objects 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 objects 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:

<B>Rutger A VosB>, <B>Jason CaravasB>, <B>Klaas HartmannB>, <B>Mark A JensenB> and <B>Chase MillerB>, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics <B>12B>:63. <http://dx.doi.org/10.1186/1471-2105-12-63>

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perl v5.20.3 BIO::PHYLO::MATRICES::DATATYPE::MIXED (3) 2014-02-08

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