NAME

Bio::Phylo::Matrices::Datatype - Superclass for objects that validate character data.

SYNOPSIS

 # No direct usage

DESCRIPTION

This is a superclass for objects that validate character data. Objects that inherit from this class (typically those in the Bio::Phylo::Matrices::Datatype::* namespace) can check strings and arrays of character data for invalid symbols, and split and join strings and arrays in a way appropriate for the type (i.e. on whitespace for continuous data, on single characters for categorical data).

METHODS

CONSTRUCTOR

new()

 Type    : Constructor
 Title   : new
 Usage   : No direct usage, is called by TypeSafaData classes;
 Function: Instantiates a Datatype object
 Returns : a Bio::Phylo::Matrices::Datatype child class
 Args    : $type (optional, one of continuous, custom, dna,
           mixed, protein, restriction, rna, standard)

MUTATORS

set_lookup()

 Type    : Mutator
 Title   : set_lookup
 Usage   : $obj->set_gap($hashref);
 Function: Sets the symbol for gaps
 Returns : Modified object.
 Args    : Argument must be a hash
           reference that maps allowed
           single character symbols
           (including ambiguity symbols)
           onto the equivalent set of
           non-ambiguous symbols

set_missing()

 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()

 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_type()

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

get_lookup()

 Type    : Accessor
 Title   : get_lookup
 Usage   : my $lookup = $obj->get_lookup;
 Function: Returns the object's lookup hash
 Returns : A hash reference
 Args    : None

get_missing()

 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()

 Type    : Accessor
 Title   : get_gap
 Usage   : my $gap = $obj->get_gap;
 Function: Returns the object's gap symbol
 Returns : A string
 Args    : None

TESTS

is_valid()

 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

is_same()

 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

UTILITY METHODS

split()

 Type    : Utility method
 Title   : split
 Usage   : $obj->split($string)
 Function: Splits $string into characters
 Returns : An array reference of characters
 Args    : A string

join()

 Type    : Utility method
 Title   : join
 Usage   : $obj->join($arrayref)
 Function: Joins $arrayref into a string
 Returns : A string
 Args    : An array reference

SEE ALSO

Bio::Phylo

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

Bio::Phylo::Manual

Also see the manual: Bio::Phylo::Manual.

FORUM

CPAN hosts a discussion forum for Bio::Phylo. If you have trouble using this module the discussion forum is a good place to start posting questions (NOT bug reports, see below): http://www.cpanforum.com/dist/Bio-Phylo

BUGS

Please report any bugs or feature requests to bug-bio-phylo@rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Phylo. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes. Be sure to include the following in your request or comment, so that I know what version you're using:

$Id: Datatype.pm 4158 2007-07-11 01:34:44Z rvosa $

AUTHOR

Rutger A. Vos,

email: rvosa@sfu.ca

web page: http://www.sfu.ca/~rvosa/

ACKNOWLEDGEMENTS

The author would like to thank Jason Stajich for many ideas borrowed from BioPerl http://www.bioperl.org, and CIPRES http://www.phylo.org and FAB* http://www.sfu.ca/~fabstar for comments and requests.

COPYRIGHT & LICENSE

Copyright 2005 Rutger A. Vos, All Rights Reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

cpanm Bio::Phylo

perl -MCPAN -e shell
install Bio::Phylo