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Bio::Phylo::Matrices::Datatype(3) User Contributed Perl Documentation Bio::Phylo::Matrices::Datatype(3)

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

 # No direct usage

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.

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)
    

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
    

get_type()
Gets data type 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_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 object's 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 object's 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 object's 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
    

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
    

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
    

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
    

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>.

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>

2017-10-30 perl v5.32.1

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