Bio::Phylo::Matrices::Matrix - Character state matrix
use Bio::Phylo::Factory;
my $fac = Bio::Phylo::Factory->new;
# instantiate taxa object
my $taxa = $fac->create_taxa;
for ( 'Homo sapiens', 'Pan paniscus', 'Pan troglodytes' ) {
$taxa->insert( $fac->create_taxon( '-name' => $_ ) );
}
# instantiate matrix object, 'standard' data type. All categorical
# data types follow semantics like this, though with different
# symbols in lookup table and matrix
my $standard_matrix = $fac->create_matrix(
'-type' => 'STANDARD',
'-taxa' => $taxa,
'-lookup' => {
'-' => [],
'0' => [ '0' ],
'1' => [ '1' ],
'?' => [ '0', '1' ],
},
'-labels' => [ 'Opposable big toes', 'Opposable thumbs', 'Not a pygmy' ],
'-matrix' => [
[ 'Homo sapiens' => '0', '1', '1' ],
[ 'Pan paniscus' => '1', '1', '0' ],
[ 'Pan troglodytes' => '1', '1', '1' ],
],
);
# note: complicated constructor for mixed data!
my $mixed_matrix = Bio::Phylo::Matrices::Matrix->new(
# if you want to create 'mixed', value for '-type' is array ref...
'-type' => [
# ...with first field 'mixed'...
'mixed',
# ...second field is an array ref...
[
# ...with _ordered_ key/value pairs...
'dna' => 10, # value is length of type range
'standard' => 10, # value is length of type range
# ... or, more complicated, value is a hash ref...
'rna' => {
'-length' => 10, # value is length of type range
# ...value for '-args' is an array ref with args
# as can be passed to 'unmixed' datatype constructors,
# for example, here we modify the lookup table for
# rna to allow both 'U' (default) and 'T'
'-args' => [
'-lookup' => {
'A' => [ 'A' ],
'C' => [ 'C' ],
'G' => [ 'G' ],
'U' => [ 'U' ],
'T' => [ 'T' ],
'M' => [ 'A', 'C' ],
'R' => [ 'A', 'G' ],
'S' => [ 'C', 'G' ],
'W' => [ 'A', 'U', 'T' ],
'Y' => [ 'C', 'U', 'T' ],
'K' => [ 'G', 'U', 'T' ],
'V' => [ 'A', 'C', 'G' ],
'H' => [ 'A', 'C', 'U', 'T' ],
'D' => [ 'A', 'G', 'U', 'T' ],
'B' => [ 'C', 'G', 'U', 'T' ],
'X' => [ 'G', 'A', 'U', 'T', 'C' ],
'N' => [ 'G', 'A', 'U', 'T', 'C' ],
},
],
},
],
],
);
# prints 'mixed(Dna:1-10, Standard:11-20, Rna:21-30)'
print $mixed_matrix->get_type;
This module defines a container object that holds Bio::Phylo::Matrices::Datum objects. The matrix object inherits from Bio::Phylo::Listable, so the methods defined there apply here.
Matrix constructor.
Type : Constructor
Title : new
Usage : my $matrix = Bio::Phylo::Matrices::Matrix->new;
Function: Instantiates a Bio::Phylo::Matrices::Matrix
object.
Returns : A Bio::Phylo::Matrices::Matrix object.
Args : -type => optional, but if used must be FIRST argument,
defines datatype, one of dna|rna|protein|
continuous|standard|restriction|[ mixed => [] ]
-taxa => optional, link to taxa object
-lookup => character state lookup hash ref
-labels => array ref of character labels
-matrix => two-dimensional array, first element of every
row is label, subsequent are characters
Matrix constructor from Bio::Align::AlignI argument.
Type : Constructor
Title : new_from_bioperl
Usage : my $matrix =
Bio::Phylo::Matrices::Matrix->new_from_bioperl(
$aln
);
Function: Instantiates a
Bio::Phylo::Matrices::Matrix object.
Returns : A Bio::Phylo::Matrices::Matrix object.
Args : An alignment that implements Bio::Align::AlignI
Sets three special symbols in one call
Type : Mutator
Title : set_special_symbols
Usage : $matrix->set_special_symbols(
-missing => '?',
-gap => '-',
-matchchar => '.'
);
Function: Assigns state labels.
Returns : $self
Args : Three args (with distinct $x, $y and $z):
-missing => $x,
-gap => $y,
-matchchar => $z
Notes : This method is here to ensure
you don't accidentally use the
same symbol for missing AND gap
Sets argument state labels.
Type : Mutator
Title : set_statelabels
Usage : $matrix->set_statelabels( [ [ 'state1', 'state2' ] ] );
Function: Assigns state labels.
Returns : $self
Args : ARRAY, or nothing (to reset);
The array is two-dimensional,
the first index is to indicate
the column the labels apply to,
the second dimension the states
(sorted numerically or alphabetically,
depending on what's appropriate)
Sets argument character labels.
Type : Mutator Title : set_charlabels Usage : $matrix->set_charlabels( [ 'char1', 'char2', 'char3' ] ); Function: Assigns character labels. Returns : $self Args : ARRAY, or nothing (to reset);
Defines matrix gapmode.
Type : Mutator Title : set_gapmode Usage : $matrix->set_gapmode( 1 ); Function: Defines matrix gapmode ( false = missing, true = fifth state ) Returns : $self Args : boolean
Assigns match symbol.
Type : Mutator Title : set_matchchar Usage : $matrix->set_matchchar( $match ); Function: Assigns match symbol (default is '.'). Returns : $self Args : ARRAY
Defines matrix 'polymorphism' interpretation.
Type : Mutator
Title : set_polymorphism
Usage : $matrix->set_polymorphism( 1 );
Function: Defines matrix 'polymorphism' interpretation
( false = uncertainty, true = polymorphism )
Returns : $self
Args : boolean
Set contents using two-dimensional array argument.
Type : Mutator
Title : set_raw
Usage : $matrix->set_raw( [ [ 'taxon1' => 'acgt' ], [ 'taxon2' => 'acgt' ] ] );
Function: Syntax sugar to define $matrix data contents.
Returns : $self
Args : A two-dimensional array; first dimension contains matrix rows,
second dimension contains taxon name / character string pair.
Defines matrix case sensitivity interpretation.
Type : Mutator
Title : set_respectcase
Usage : $matrix->set_respectcase( 1 );
Function: Defines matrix case sensitivity interpretation
( false = disregarded, true = "respectcase" )
Returns : $self
Args : boolean
Retrieves hash ref for missing, gap and matchchar symbols
Type : Accessor
Title : get_special_symbols
Usage : my %syms = %{ $matrix->get_special_symbols };
Function: Retrieves special symbols
Returns : HASH ref, e.g. { -missing => '?', -gap => '-', -matchchar => '.' }
Args : None.
Retrieves state labels.
Type : Accessor
Title : get_statelabels
Usage : my @statelabels = @{ $matrix->get_statelabels };
Function: Retrieves state labels.
Returns : ARRAY
Args : None.
Retrieves character labels.
Type : Accessor
Title : get_charlabels
Usage : my @charlabels = @{ $matrix->get_charlabels };
Function: Retrieves character labels.
Returns : ARRAY
Args : None.
Returns matrix gapmode.
Type : Accessor Title : get_gapmode Usage : do_something() if $matrix->get_gapmode; Function: Returns matrix gapmode ( false = missing, true = fifth state ) Returns : boolean Args : none
Returns matrix match character.
Type : Accessor Title : get_matchchar Usage : my $char = $matrix->get_matchchar; Function: Returns matrix match character (default is '.') Returns : SCALAR Args : none
Calculates number of characters.
Type : Accessor
Title : get_nchar
Usage : my $nchar = $matrix->get_nchar;
Function: Calculates number of characters (columns) in matrix (if the matrix
is non-rectangular, returns the length of the longest row).
Returns : INT
Args : none
Calculates number of taxa (rows) in matrix.
Type : Accessor Title : get_ntax Usage : my $ntax = $matrix->get_ntax; Function: Calculates number of taxa (rows) in matrix Returns : INT Args : none
Returns matrix 'polymorphism' interpretation.
Type : Accessor
Title : get_polymorphism
Usage : do_something() if $matrix->get_polymorphism;
Function: Returns matrix 'polymorphism' interpretation
( false = uncertainty, true = polymorphism )
Returns : boolean
Args : none
Retrieves a 'raw' (two-dimensional array) representation of the matrix's contents.
Type : Accessor
Title : get_raw
Usage : my $rawmatrix = $matrix->get_raw;
Function: Retrieves a 'raw' (two-dimensional array) representation
of the matrix's contents.
Returns : A two-dimensional array; first dimension contains matrix rows,
second dimension contains taxon name and characters.
Args : NONE
Returns matrix case sensitivity interpretation.
Type : Accessor
Title : get_respectcase
Usage : do_something() if $matrix->get_respectcase;
Function: Returns matrix case sensitivity interpretation
( false = disregarded, true = "respectcase" )
Returns : boolean
Args : none
Creates bootstrapped clone.
Type : Utility method
Title : bootstrap
Usage : my $bootstrap = $object->bootstrap;
Function: Creates bootstrapped clone.
Returns : A bootstrapped clone of the invocant.
Args : NONE
Comments: The bootstrapping algorithm uses perl's random number
generator to create a new series of indices (without
replacement) of the same length as the original matrix.
These indices are first sorted, then applied to the
cloned sequences. Annotations (if present) stay connected
to the resampled cells.
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
Serializes matrix to nexml format.
Type : Format convertor
Title : to_xml
Usage : my $data_block = $matrix->to_xml;
Function: Converts matrix object into a nexml element structure.
Returns : Nexml block (SCALAR).
Args : Optional:
-compact => 1 (for compact representation of matrix)
Serializes matrix to nexus format.
Type : Format convertor
Title : to_nexus
Usage : my $data_block = $matrix->to_nexus;
Function: Converts matrix object into a nexus data block.
Returns : Nexus data block (SCALAR).
Args : The following options are available:
# if set, writes TITLE & LINK tokens
'-links' => 1
# if set, writes block as a "data" block (deprecated, but used by mrbayes),
# otherwise writes "characters" block (default)
-data_block => 1
# if set, writes "RESPECTCASE" token
-respectcase => 1
# if set, writes "GAPMODE=(NEWSTATE or MISSING)" token
-gapmode => 1
# if set, writes "MSTAXA=(POLYMORPH or UNCERTAIN)" token
-polymorphism => 1
# if set, writes character labels
-charlabels => 1
# if set, writes state labels
-statelabels => 1
# if set, writes mesquite-style charstatelabels
-charstatelabels => 1
# by default, names for sequences are derived from $datum->get_name, if
# 'internal' is specified, uses $datum->get_internal_name, if 'taxon'
# uses $datum->get_taxon->get_name, if 'taxon_internal' uses
# $datum->get_taxon->get_internal_name, if $key, uses $datum->get_generic($key)
-seqnames => one of (internal|taxon|taxon_internal|$key)
Insert argument in invocant.
Type : Listable method
Title : insert
Usage : $matrix->insert($datum);
Function: Inserts $datum in $matrix.
Returns : Modified object
Args : A datum object
Comments: This method re-implements the method by the same
name in Bio::Phylo::Listable
Validates the object's contents.
Type : Method
Title : validate
Usage : $obj->validate
Function: Validates the object's contents
Returns : True or throws Bio::Phylo::Util::Exceptions::InvalidData
Args : None
Comments: This method implements the interface method by the same
name in Bio::Phylo::Matrices::TypeSafeData
Removes unused states from lookup table
Type : Method Title : validate Usage : $obj->compress_lookup Function: Removes unused states from lookup table Returns : $self Args : None
Validates taxa associations.
Type : Method
Title : check_taxa
Usage : $obj->check_taxa
Function: Validates relation between matrix and taxa block
Returns : Modified object
Args : None
Comments: This method implements the interface method by the same
name in Bio::Phylo::Taxa::TaxaLinker
Creates a taxa block from the objects contents if none exists yet.
Type : Method Title : make_taxa Usage : my $taxa = $obj->make_taxa Function: Creates a taxa block from the objects contents if none exists yet. Returns : $taxa Args : NONE
Bio::Phylo::Matrices::Matrix inherits from one or more superclasses. This means that objects of class Bio::Phylo::Matrices::Matrix 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::Matrix inherits from superclass Bio::Phylo::Matrices::TypeSafeData. 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
Get 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 ambiguity 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 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 data type.
Type : Accessor Title : get_type Usage : my $type = $obj->get_type; Function: Returns the object's datatype Returns : A string Args : None
Get data type object.
Type : Accessor Title : get_type_object Usage : my $obj = $obj->get_type_object; Function: Returns the object's linked datatype object Returns : A subclass of Bio::Phylo::Matrices::Datatype Args : None
TypeSafeData constructor.
Type : Constructor
Title : new
Usage : No direct usage, is called by child class;
Function: Instantiates a Bio::Phylo::Matrices::TypeSafeData
Returns : a Bio::Phylo::Matrices::TypeSafeData child class
Args : -type => (data type - required)
Optional:
-missing => (the symbol for missing data)
-gap => (the symbol for gaps)
-lookup => (a character state lookup hash)
-type_object => (a datatype object)
Set gap data 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 ambiguity lookup table.
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 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 data type.
Type : Mutator
Title : set_type
Usage : $obj->set_type($type);
Function: Sets the object's datatype.
Returns : Modified object.
Args : Argument must be a string, one of
continuous, custom, dna, mixed,
protein, restriction, rna, standard
Set data type object.
Type : Mutator
Title : set_type_object
Usage : $obj->set_gap($obj);
Function: Sets the datatype object
Returns : Modified object.
Args : Argument must be a subclass
of Bio::Phylo::Matrices::Datatype
Validates the object's contents
Type : Interface method
Title : validate
Usage : $obj->validate
Function: Validates the object's contents
Returns : True or throws Bio::Phylo::Util::Exceptions::InvalidData
Args : None
Comments: This is an interface method, i.e. this class doesn't
implement the method, child classes have to
Bio::Phylo::Matrices::Matrix inherits from superclass Bio::Phylo::Listable. Below are the public methods (if any) from this superclass.
Type : Mutator Title : add_set Usage : $obj->add_set($set) Function: Associates a Bio::Phylo::Set object with the invocant Returns : Invocant Args : A Bio::Phylo::Set object
Type : Mutator
Title : add_to_set
Usage : $listable->add_to_set($obj,$set);
Function: Adds first argument to the second argument
Returns : Invocant
Args : $obj - an object to add to $set
$set - the Bio::Phylo::Set object to add to
Notes : this method assumes that $obj is already
part of the invocant. If that assumption is
violated a warning message is printed.
Tests if argument can be inserted in invocant.
Type : Test Title : can_contain Usage : &do_something if $listable->can_contain( $obj ); Function: Tests if $obj can be inserted in $listable Returns : BOOL Args : An $obj to test
Empties container object.
Type : Object method Title : clear Usage : $obj->clear(); Function: Clears the container. Returns : A Bio::Phylo::Listable object. Args : Note. Note :
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.
Tests whether the invocant object contains the argument object.
Type : Test
Title : contains
Usage : if ( $obj->contains( $other_obj ) ) {
# do something
}
Function: Tests whether the invocant object
contains the argument object
Returns : BOOLEAN
Args : A Bio::Phylo::* object
The cross_reference method links node and datum objects to the taxa they apply to. After crossreferencing a matrix with a taxa object, every datum object has a reference to a taxon object stored in its $datum->get_taxon field, and every taxon object has a list of references to datum objects stored in its $taxon->get_data field.
Type : Generic method
Title : cross_reference
Usage : $obj->cross_reference($taxa);
Function: Crossreferences the entities
in the invocant with names
in $taxa
Returns : string
Args : A Bio::Phylo::Taxa object
Comments:
Returns the current focal element of the listable object.
Type : Iterator
Title : current
Usage : my $current_obj = $obj->current;
Function: Retrieves the current focal
entity in the invocant.
Returns : A Bio::Phylo::* object
Args : none.
Returns the current internal index of the invocant.
Type : Generic query
Title : current_index
Usage : my $last_index = $obj->current_index;
Function: Returns the current internal
index of the invocant.
Returns : An integer
Args : none.
Deletes argument from invocant object.
Type : Object method
Title : delete
Usage : $obj->delete($other_obj);
Function: Deletes an object from its container.
Returns : A Bio::Phylo::Listable object.
Args : A Bio::Phylo::* object.
Note : Be careful with this method: deleting
a node from a tree like this will
result in undefined references in its
neighbouring nodes. Its children will
have their parent reference become
undef (instead of pointing to their
grandparent, as collapsing a node would
do). The same is true for taxon objects
that reference datum objects: if the
datum object is deleted from a matrix
(say), the taxon will now hold undefined
references.
Jumps to the first element contained by the listable object.
Type : Iterator
Title : first
Usage : my $first_obj = $obj->first;
Function: Retrieves the first
entity in the invocant.
Returns : A Bio::Phylo::* object
Args : none.
Gets element defined by argument index from invocant container.
Type : Query
Title : get_by_index
Usage : my $contained_obj = $obj->get_by_index($i);
Function: Retrieves the i'th entity
from a listable object.
Returns : An entity stored by a listable
object (or array ref for slices).
Args : An index or range. This works
the way you dereference any perl
array including through slices,
i.e. $obj->get_by_index(0 .. 10)>
$obj->get_by_index(0, -1)
and so on.
Comments: Throws if out-of-bounds
Gets first element that has argument name
Type : Visitor predicate
Title : get_by_name
Usage : my $found = $obj->get_by_name('foo');
Function: Retrieves the first contained object
in the current Bio::Phylo::Listable
object whose name is 'foo'
Returns : A Bio::Phylo::* object.
Args : A name (string)
Gets elements that match regular expression from invocant container.
Type : Visitor predicate
Title : get_by_regular_expression
Usage : my @objects = @{
$obj->get_by_regular_expression(
-value => $method,
-match => $re
) };
Function: Retrieves the data in the
current Bio::Phylo::Listable
object whose $method output
matches $re
Returns : A list of Bio::Phylo::* objects.
Args : -value => any of the string
datum props (e.g. 'get_type')
-match => a compiled regular
expression (e.g. qr/^[D|R]NA$/)
Gets elements that meet numerical rule from invocant container.
Type : Visitor predicate
Title : get_by_value
Usage : my @objects = @{ $obj->get_by_value(
-value => $method,
-ge => $number
) };
Function: Iterates through all objects
contained by $obj and returns
those for which the output of
$method (e.g. get_tree_length)
is less than (-lt), less than
or equal to (-le), equal to
(-eq), greater than or equal to
(-ge), or greater than (-gt) $number.
Returns : A reference to an array of objects
Args : -value => any of the numerical
obj data (e.g. tree length)
-lt => less than
-le => less than or equals
-eq => equals
-ge => greater than or equals
-gt => greater than
Returns a reference to an array of objects contained by the listable object.
Type : Generic query
Title : get_entities
Usage : my @entities = @{ $obj->get_entities };
Function: Retrieves all entities in the invocant.
Returns : A reference to a list of Bio::Phylo::*
objects.
Args : none.
Returns the index of the argument in the list, or undef if the list doesn't contain the argument
Type : Generic query
Title : get_index_of
Usage : my $i = $listable->get_index_of($obj)
Function: Returns the index of the argument in the list,
or undef if the list doesn't contain the argument
Returns : An index or undef
Args : A contained object
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
Type : Accessor
Title : get_sets
Usage : my @sets = @{ $obj->get_sets() };
Function: Retrieves all associated Bio::Phylo::Set objects
Returns : Invocant
Args : None
Pushes an object into its container.
Type : Object method Title : insert Usage : $obj->insert($other_obj); Function: Pushes an object into its container. Returns : A Bio::Phylo::Listable object. Args : A Bio::Phylo::* object.
Inserts argument object in invocant container at argument index.
Type : Object method Title : insert_at_index Usage : $obj->insert_at_index($other_obj, $i); Function: Inserts $other_obj at index $i in container $obj Returns : A Bio::Phylo::Listable object. Args : A Bio::Phylo::* object.
Type : Test
Title : is_in_set
Usage : @do_something if $listable->is_in_set($obj,$set);
Function: Returns whether or not the first argument is listed in the second argument
Returns : Boolean
Args : $obj - an object that may, or may not be in $set
$set - the Bio::Phylo::Set object to query
Notes : This method makes two assumptions:
i) the $set object is associated with the invocant,
i.e. add_set($set) has been called previously
ii) the $obj object is part of the invocant
If either assumption is violated a warning message
is printed.
Jumps to the last element contained by the listable object.
Type : Iterator
Title : last
Usage : my $last_obj = $obj->last;
Function: Retrieves the last
entity in the invocant.
Returns : A Bio::Phylo::* object
Args : none.
Returns the highest valid index of the invocant.
Type : Generic query
Title : last_index
Usage : my $last_index = $obj->last_index;
Function: Returns the highest valid
index of the invocant.
Returns : An integer
Args : none.
Returns the next focal element of the listable object.
Type : Iterator
Title : next
Usage : my $next_obj = $obj->next;
Function: Retrieves the next focal
entity in the invocant.
Returns : A Bio::Phylo::* object
Args : none.
Notifies listeners of changed contents.
Type : Utility method Title : notify_listeners Usage : $object->notify_listeners; Function: Notifies listeners of changed contents. Returns : Invocant. Args : NONE. Comments:
Returns the previous element of the listable object.
Type : Iterator
Title : previous
Usage : my $previous_obj = $obj->previous;
Function: Retrieves the previous
focal entity in the invocant.
Returns : A Bio::Phylo::* object
Args : none.
Type : Mutator
Title : remove_from_set
Usage : $listable->remove_from_set($obj,$set);
Function: Removes first argument from the second argument
Returns : Invocant
Args : $obj - an object to remove from $set
$set - the Bio::Phylo::Set object to remove from
Notes : this method assumes that $obj is already
part of the invocant. If that assumption is
violated a warning message is printed.
Type : Mutator Title : remove_set Usage : $obj->remove_set($set) Function: Removes association between a Bio::Phylo::Set object and the invocant Returns : Invocant Args : A Bio::Phylo::Set object
Attaches a listener (code ref) which is executed when contents change.
Type : Utility method
Title : set_listener
Usage : $object->set_listener( sub { my $object = shift; } );
Function: Attaches a listener (code ref) which is executed when contents change.
Returns : Invocant.
Args : A code reference.
Comments: When executed, the code reference will receive $object
(the invocant) as its first argument.
Iterates over objects contained by invocant, executes argument code reference on each.
Type : Visitor predicate
Title : visit
Usage : $obj->visit(
sub{ print $_[0]->get_name, "\n" }
);
Function: Implements visitor pattern
using code reference.
Returns : The invocant, possibly modified.
Args : a CODE reference.
Bio::Phylo::Matrices::Matrix 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::Matrix 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
Bio::Phylo::Matrices::Matrix inherits from superclass Bio::Phylo::Taxa::TaxaLinker. Below are the public methods (if any) from this superclass.
Performs sanity check on taxon relationships.
Type : Interface method Title : check_taxa Usage : $obj->check_taxa Function: Performs sanity check on taxon relationships Returns : $obj Args : NONE
Retrieves association between invocant and Bio::Phylo::Taxa object.
Type : Accessor
Title : get_taxa
Usage : my $taxa = $obj->get_taxa;
Function: Retrieves the Bio::Phylo::Taxa
object linked to the invocant.
Returns : Bio::Phylo::Taxa
Args : NONE
Comments: This method returns the Bio::Phylo::Taxa
object to which the invocant is linked.
The returned object can therefore contain
*more* taxa than are actually in the matrix.
Creates a taxa block from the objects contents if none exists yet.
Type : Decorated interface method Title : make_taxa Usage : my $taxa = $obj->make_taxa Function: Creates a taxa block from the objects contents if none exists yet. Returns : $taxa Args : NONE
Associates invocant with Bio::Phylo::Taxa argument.
Type : Mutator
Title : set_taxa
Usage : $obj->set_taxa( $taxa );
Function: Links the invocant object
to a taxa object.
Returns : Modified $obj
Args : A Bio::Phylo::Taxa object.
Removes association between invocant and Bio::Phylo::Taxa object.
Type : Mutator Title : unset_taxa Usage : $obj->unset_taxa(); Function: Removes the link between invocant object and taxa Returns : Modified $obj Args : NONE
This object inherits from Bio::Phylo::Taxa::TaxaLinker, so the methods defined therein are also applicable to Bio::Phylo::Matrices::Matrix objects.
This object inherits from Bio::Phylo::Matrices::TypeSafeData, so the methods defined therein are also applicable to Bio::Phylo::Matrices::Matrix objects.
Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com.
$Id: Matrix.pm 844 2009-03-05 00:07:26Z rvos $
