GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages


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

.ds Aq ’

NAME

Bio::Phylo::Matrices::Datatype - Validator of character state data

CONTENTS

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 (on whitespace for continuous data, on single characters for categorical data). Bio::Phylo::Matrices::Matrix objects and Bio::Phylo::Matrices::Datum internally delegate validation of their contents to these datatype objects; there is no normal usage in which you’d have to deal with datatype objects directly.

METHODS

    CONSTRUCTOR

new() Datatype constructor.



 Type    : Constructor
 Title   : new
 Usage   : No direct usage, is called by TypeSafeData 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() Sets state lookup table.



 Type    : Mutator
 Title   : set_lookup
 Usage   : $obj->set_lookup($hashref);
 Function: Sets the state lookup table.
 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() Sets missing data symbol.



 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 gap symbol.



 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 -



set_metas_for_states() Assigns all metadata annotations for all state symbols



 Type    : Mutator
 Title   : set_metas_for_states
 Usage   : $obj->set_metas_for_states({ $state => [ $m1, $m2 ] });
 Function: Assigns all metadata annotations for all state symbols
 Returns : Modified object.
 Args    : A hash reference of state symbols with metadata arrays



add_meta_for_state() Adds a metadata annotation for a state symbol



 Type    : Mutator
 Title   : add_meta_for_state
 Usage   : $obj->add_meta_for_state($meta,$state);
 Function: Adds a metadata annotation for a state symbol
 Returns : Modified object.
 Args    : A Bio::Phylo::NeXML::Meta object and a state symbol



remove_meta_for_state() Removes a metadata annotation for a state symbol



 Type    : Mutator
 Title   : remove_meta_for_state
 Usage   : $obj->remove_meta_for_state($meta,$state);
 Function: Removes a metadata annotation for a state symbol
 Returns : Modified object.
 Args    : A Bio::Phylo::NeXML::Meta object and a state symbol



    ACCESSORS

get_type() Gets data type as string.



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



get_ids_for_special_symbols() Gets state-to-id mapping for missing and gap symbols



 Type    : Accessor
 Title   : get_ids_for_special_symbols
 Usage   : my %ids = %{ $obj->get_ids_for_special_symbols };
 Function: Returns state-to-id mapping
 Returns : A hash reference, keyed on symbol, with UID values
 Args    : Optional, a boolean:
           true  => prefix state ids with s
           false => keep ids numerical



get_ids_for_states() Gets state-to-id mapping



 Type    : Accessor
 Title   : get_ids_for_states
 Usage   : my %ids = %{ $obj->get_ids_for_states };
 Function: Returns state-to-id mapping
 Returns : A hash reference, keyed on symbol, with UID values
 Args    : Optional, a boolean:
           true  => prefix state ids with s
           false => keep ids numerical
 Note    : This returns a mapping to alphanumeric states; special
           symbols (for missing data and gaps) are handled separately



get_states_for_symbol() Gets set of fundamental states for an ambiguity symbol



 Type    : Accessor
 Title   : get_states_for_symbol
 Usage   : my @states = @{ $obj->get_states_for_symbol(N) };
 Function: Returns the set of states for an ambiguity symbol
 Returns : An array ref of symbols
 Args    : An ambiguity symbol
 Comments: If supplied argument is a fundamental state, an array
           ref with just that state is returned, e.g. A returns
           [A] for DNA and RNA



get_symbol_for_states() Gets ambiguity symbol for a set of states



 Type    : Accessor
 Title   : get_symbol_for_states
 Usage   : my $state = $obj->get_symbol_for_states(A,C);
 Function: Returns the ambiguity symbol for a set of states
 Returns : A symbol (SCALAR)
 Args    : A set of symbols
 Comments: If no symbol exists in the lookup
           table for the given set of states,
           a new - numerical - one is created



get_lookup() Gets state lookup table.



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



get_missing() Gets 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() Gets 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_meta_for_state() Gets metadata annotations (if any) for the provided state symbol



 Type    : Accessor
 Title   : get_meta_for_state
 Usage   : my @meta = @{ $obj->get_meta_for_state };
 Function: Gets metadata annotations for a state symbol
 Returns : An array reference of Bio::Phylo::NeXML::Meta objects
 Args    : A state symbol



get_metas_for_states() Gets metadata annotations (if any) for all state symbols



 Type    : Accessor
 Title   : get_metas_for_states
 Usage   : my @meta = @{ $obj->get_metas_for_states };
 Function: Gets metadata annotations for state symbols
 Returns : An array reference of Bio::Phylo::NeXML::Meta objects
 Args    : None



    TESTS

is_ambiguous() Tests whether the supplied state symbol represents an ambiguous (polymorphic or uncertain) state. For example, for the most commonly-used alphabet for DNA states, the symbol ’N’ represents complete uncertainty, the actual state could be any of ’A’, ’C’, ’G’ or ’T’, and so this method would return a true value.



 Type    : Test
 Title   : is_ambiguous
 Usage   : if ( $obj->is_ambiguous(N) ) {
              # do something
           }
 Function: Returns true if argument is an ambiguous state symbol
 Returns : BOOLEAN
 Args    : A state symbol



is_valid() Validates argument.



 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() 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



    UTILITY METHODS

split() Splits argument string of characters following appropriate rules.



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



join() Joins argument array ref of characters following appropriate rules.



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



    SERIALIZERS

to_xml() Writes data type definitions to xml



 Type    : Serializer
 Title   : to_xml
 Usage   : my $xml = $obj->to_xml
 Function: Writes data type definitions to xml
 Returns : An xml string representation of data type definition
 Args    : None



to_dom() Analog to to_xml.



 Type    : Serializer
 Title   : to_dom
 Usage   : $type->to_dom
 Function: Generates a DOM subtree from the invocant
           and its contained objects
 Returns : an <XML Package>::Element object
 Args    : none



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 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 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>

Search for    or go to Top of page |  Section 3 |  Main Index


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

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with manServer 1.07.