Bio::Phylo::Matrices::Datatype::Continuous - Validator subclass, no serviceable parts inside
The Bio::Phylo::Matrices::Datatype::* classes are used to validated data contained by Bio::Phylo::Matrices::Matrix and Bio::Phylo::Matrices::Datum objects.
Sets the lookup table (no-op for continuous data!).
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
Gets the lookup table (no-op for continuous data!).
Type : Accessor Title : get_lookup Usage : my $lookup = $obj->get_lookup; Function: Returns the object's lookup hash Returns : A hash reference Args : None
Validates arguments for data validity.
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 list of Bio::Phylo::Matrices::Datum object, and/or
character array references, and/or character strings,
and/or single characters
Splits string of characters on whitespaces.
Type : Utility method Title : split Usage : $obj->split($string) Function: Splits $string into characters Returns : An array reference of characters Args : A string
Joins array ref of characters to a space-separated string.
Type : Utility method Title : join Usage : $obj->join($arrayref) Function: Joins $arrayref into a string Returns : A string Args : An array reference
Bio::Phylo::Matrices::Datatype::Continuous inherits from one or more superclasses. This means that objects of class Bio::Phylo::Matrices::Datatype::Continuous also "do" the methods from the superclasses in addition to the ones implemented in this class. Below is the documentation for those additional methods, organized by superclass.
Bio::Phylo::Matrices::Datatype::Continuous inherits from superclass Bio::Phylo::Matrices::Datatype. Below are the public methods (if any) from this superclass.
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
Gets state-to-id mapping
Type : Accessor
Title : get_ids_for_states
Usage : my %ids = %{ $obj->get_ids_for_states };
Function: Returns the object's datatype
Returns : A hash reference, keyed on state, with UID values
Args : None
Gets a logger object.
Type : Accessor Title : get_logger Usage : my $logger = $obj->get_logger; Function: Returns a Bio::Phylo::Util::Logger object Returns : Bio::Phylo::Util::Logger Args : None
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
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
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
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
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
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
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
The Bio::Phylo root constructor, is rarely used directly. Rather, many other objects in Bio::Phylo internally go up the inheritance tree to this constructor. The arguments shown here can therefore also be passed to any of the child classes' constructors, which will pass them on up the inheritance tree. Generally, constructors in Bio::Phylo subclasses can process as arguments all methods that have set_* in their names. The arguments are named for the methods, but "set_" has been replaced with a dash "-", e.g. the method "set_name" becomes the argument "-name" in the constructor.
Type : Constructor
Title : new
Usage : my $phylo = Bio::Phylo->new;
Function: Instantiates Bio::Phylo object
Returns : a Bio::Phylo object
Args : Optional, any number of setters. For example,
Bio::Phylo->new( -name => $name )
will call set_name( $name ) internally
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 '-'
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
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 '?'
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
Serializes invocant to XML.
Type : XML serializer Title : to_xml Usage : my $xml = $obj->to_xml; Function: Serializes $obj to xml Returns : An xml string Args : None
Bio::Phylo::Matrices::Datatype::Continuous inherits from superclass Bio::Phylo::Util::XMLWritable. Below are the public methods (if any) from this superclass.
Type : Mutator Title : add_dictionary Usage : $obj->add_dictionary($dict); Function: Adds a dictionary attachment to the object Returns : $self Args : Bio::Phylo::Dictionary
Retrieves attributes for the element.
Type : Accessor
Title : get_attributes
Usage : my %attrs = %{ $obj->get_attributes };
Function: Gets the xml attributes for the object;
Returns : A hash reference
Args : None.
Comments: throws ObjectMismatch if no linked taxa object
can be found
Retrieves the dictionaries for the element.
Type : Accessor
Title : get_dictionaries
Usage : my @dicts = @{ $obj->get_dictionaries };
Function: Retrieves the dictionaries for the element.
Returns : An array ref of Bio::Phylo::Dictionary objects
Args : None.
Type : Accessor
Title : get_namespaces
Usage : my %ns = %{ $obj->get_namespaces };
Function: Retrieves the known namespaces
Returns : A hash of prefix/namespace key/value pairs, or
a single namespace if a single, optional
prefix was provided as argument
Args : Optional - a namespace prefix
Retrieves tag name for the element.
Type : Accessor Title : get_tag Usage : my $tag = $obj->get_tag; Function: Gets the xml tag name for the object; Returns : A tag name Args : None.
Retrieves xml id for the element.
Type : Accessor Title : get_xml_id Usage : my $id = $obj->get_xml_id; Function: Gets the xml id for the object; Returns : An xml id Args : None.
Retrieves tag string
Type : Accessor Title : get_xml_tag Usage : my $str = $obj->get_xml_tag; Function: Gets the xml tag for the object; Returns : A tag, i.e. pointy brackets Args : Optional: a true value, to close an empty tag
By default, all XMLWritable objects are identifiable when serialized, i.e. they have a unique id attribute. However, in some cases a serialized object may not have an id attribute (governed by the nexml schema). This method indicates whether that is the case.
Type : Test
Title : is_identifiable
Usage : if ( $obj->is_identifiable ) { ... }
Function: Indicates whether IDs are generated
Returns : BOOLEAN
Args : NONE
Type : Mutator Title : remove_dictionary Usage : $obj->remove_dictionary($dict); Function: Removes a dictionary attachment from the object Returns : $self Args : Bio::Phylo::Dictionary
Assigns attributes for the element.
Type : Mutator Title : set_attributes Usage : $obj->set_attributes( 'foo' => 'bar' ) Function: Sets the xml attributes for the object; Returns : $self Args : key/value pairs or a hash ref
By default, all XMLWritable objects are identifiable when serialized, i.e. they have a unique id attribute. However, in some cases a serialized object may not have an id attribute (governed by the nexml schema). For such objects, id generation can be explicitly disabled using this method. Typically, this is done internally - you will probably never use this method.
Type : Mutator Title : set_identifiable Usage : $obj->set_tag(0); Function: Enables/disables id generation Returns : $self Args : BOOLEAN
Type : Mutator Title : set_namespaces Usage : $obj->set_namespaces( 'dwc' => 'http://www.namespaceTBD.org/darwin2' ); Function: Adds one or more prefix/namespace pairs Returns : $self Args : One or more prefix/namespace pairs, as even-sized list, or as a hash reference, i.e.: $obj->set_namespaces( 'dwc' => 'http://www.namespaceTBD.org/darwin2' ); or $obj->set_namespaces( { 'dwc' => 'http://www.namespaceTBD.org/darwin2' } ); Notes : This is a global for the XMLWritable class, so that in a recursive to_xml call the outermost element contains the namespace definitions. This method can also be called as a static class method, i.e. Bio::Phylo::Util::XMLWritable->set_namespaces( 'dwc' => 'http://www.namespaceTBD.org/darwin2');
This method is usually only used internally, to define or alter the name of the tag into which the object is serialized. For example, for a Bio::Phylo::Forest::Node object, this method would be called with the 'node' argument, so that the object is serialized into an xml element structure called <node/>
Type : Mutator
Title : set_tag
Usage : $obj->set_tag('node');
Function: Sets the tag name
Returns : $self
Args : A tag name (must be a valid xml element name)
This method is usually only used internally, to store the xml id of an object as it is parsed out of a nexml file - this is for the purpose of round-tripping nexml info sets.
Type : Mutator
Title : set_xml_id
Usage : $obj->set_xml_id('node345');
Function: Sets the xml id
Returns : $self
Args : An xml id (must be a valid xml NCName)
Serializes invocant to XML.
Type : XML serializer Title : to_xml Usage : my $xml = $obj->to_xml; Function: Serializes $obj to xml Returns : An xml string Args : None
Bio::Phylo::Matrices::Datatype::Continuous inherits from superclass Bio::Phylo. Below are the public methods (if any) from this superclass.
Clones invocant.
Type : Utility method Title : clone Usage : my $clone = $object->clone; Function: Creates a copy of the invocant object. Returns : A copy of the invocant. Args : None. Comments: Cloning is currently experimental, use with caution.
Attempts to execute argument string as method on invocant.
Type : Accessor
Title : get
Usage : my $treename = $tree->get('get_name');
Function: Alternative syntax for safely accessing
any of the object data; useful for
interpolating runtime $vars.
Returns : (context dependent)
Args : a SCALAR variable, e.g. $var = 'get_name';
Gets invocant description.
Type : Accessor Title : get_desc Usage : my $desc = $obj->get_desc; Function: Returns the object's description (if any). Returns : A string Args : None
Gets generic hashref or hash value(s).
Type : Accessor
Title : get_generic
Usage : my $value = $obj->get_generic($key);
or
my %hash = %{ $obj->get_generic() };
Function: Returns the object's generic data. If an
argument is used, it is considered a key
for which the associated value is returned.
Without arguments, a reference to the whole
hash is returned.
Returns : A string or hash reference.
Args : None
Gets invocant's UID.
Type : Accessor Title : get_id Usage : my $id = $obj->get_id; Function: Returns the object's unique ID Returns : INT Args : None
Gets invocant's 'fallback' name (possibly autogenerated).
Type : Accessor
Title : get_internal_name
Usage : my $name = $obj->get_internal_name;
Function: Returns the object's name (if none was set, the name
is a combination of the $obj's class and its UID).
Returns : A string
Args : None
Gets a logger object.
Type : Accessor Title : get_logger Usage : my $logger = $obj->get_logger; Function: Returns a Bio::Phylo::Util::Logger object Returns : Bio::Phylo::Util::Logger Args : None
Gets invocant's name.
Type : Accessor Title : get_name Usage : my $name = $obj->get_name; Function: Returns the object's name. Returns : A string Args : None
Attempts to fetch an in-memory object by its UID
Type : Accessor Title : get_obj_by_id Usage : my $obj = Bio::Phylo->get_obj_by_id($uid); Function: Fetches an object from the IDPool cache Returns : A Bio::Phylo object Args : A unique id
Gets invocant's score.
Type : Accessor Title : get_score Usage : my $score = $obj->get_score; Function: Returns the object's numerical score (if any). Returns : A number Args : None
The Bio::Phylo root constructor, is rarely used directly. Rather, many other objects in Bio::Phylo internally go up the inheritance tree to this constructor. The arguments shown here can therefore also be passed to any of the child classes' constructors, which will pass them on up the inheritance tree. Generally, constructors in Bio::Phylo subclasses can process as arguments all methods that have set_* in their names. The arguments are named for the methods, but "set_" has been replaced with a dash "-", e.g. the method "set_name" becomes the argument "-name" in the constructor.
Type : Constructor
Title : new
Usage : my $phylo = Bio::Phylo->new;
Function: Instantiates Bio::Phylo object
Returns : a Bio::Phylo object
Args : Optional, any number of setters. For example,
Bio::Phylo->new( -name => $name )
will call set_name( $name ) internally
Sets invocant description.
Type : Mutator Title : set_desc Usage : $obj->set_desc($desc); Function: Assigns an object's description. Returns : Modified object. Args : Argument must be a string.
Sets generic key/value pair(s).
Type : Mutator
Title : set_generic
Usage : $obj->set_generic( %generic );
Function: Assigns generic key/value pairs to the invocant.
Returns : Modified object.
Args : Valid arguments constitute:
* key/value pairs, for example:
$obj->set_generic( '-lnl' => 0.87565 );
* or a hash ref, for example:
$obj->set_generic( { '-lnl' => 0.87565 } );
* or nothing, to reset the stored hash, e.g.
$obj->set_generic( );
Sets invocant name.
Type : Mutator
Title : set_name
Usage : $obj->set_name($name);
Function: Assigns an object's name.
Returns : Modified object.
Args : Argument must be a string, will be single
quoted if it contains [;|,|:\(|\)]
or spaces. Preceding and trailing spaces
will be removed.
Sets invocant score.
Type : Mutator
Title : set_score
Usage : $obj->set_score($score);
Function: Assigns an object's numerical score.
Returns : Modified object.
Args : Argument must be any of
perl's number formats, or undefined
to reset score.
Serializes object to JSON string
Type : Serializer Title : to_json() Usage : print $obj->to_json(); Function: Serializes object to JSON string Returns : String Args : None Comments:
Serializes object to general purpose string
Type : Serializer Title : to_string() Usage : print $obj->to_string(); Function: Serializes object to general purpose string Returns : String Args : None Comments: This is YAML
This object inherits from Bio::Phylo::Matrices::Datatype, so the methods defined therein are also applicable to Bio::Phylo::Matrices::Datatype::Continuous objects.
Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com.
$Id: Continuous.pm 844 2009-03-05 00:07:26Z rvos $
