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Bio-Phylo-0.13
River stage two • 9 direct dependents • 18 total dependents
8 ++
/ Bio::Phylo::Matrices::Matrix

NAME

Bio::Phylo::Matrices::Matrix - Character state matrix, implements Bio::CDAT::CharMatrixI

SYNOPSIS

 use Bio::Phylo::Matrices::Matrix;
 use Bio::Phylo::Taxa;
 use Bio::Phylo::Taxa::Taxon;

 # instantiate taxa object
 my $taxa = Bio::Phylo::Taxa->new();
 for ( 'Homo sapiens', 'Pan paniscus', 'Pan troglodytes' ) {
     $taxa->insert( Bio::Phylo::Taxa::Taxon->new( '-name' => $_ ) );
 }

 # instantiate matrix object
 my $matrix = Bio::Phylo::Matrices::Matrix->new(
     '-taxa'   => $taxa,
     '-type'   => 'STANDARD',
     '-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' ],
     ],
 );

DESCRIPTION

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.

METHODS

CONSTRUCTOR

new()
 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   => required, 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

MUTATORS

set_taxa()
 Type    : Mutator
 Title   : set_taxa
 Usage   : $matrix->set_taxa( $taxa );
 Function: Links the invocant matrix object
           to a taxa object. Individual datum
           objects are linked to individual taxon
           objects by name, i.e. by what is
           returned by $datum->get_name
 Returns : $matrix
 Args    : A Bio::Phylo::Taxa object.
 Comments: This method checks whether any
           of the datum objects in the
           invocant link to Bio::Phylo::Taxa::Taxon
           objects not contained by $matrix. If
           found, these are set to undef and the
           following message is displayed:

           "Reset X references from datum objects
           to taxa outside taxa block"
set_charlabels()
 Type    : Mutator
 Title   : set_charlabels
 Usage   : $matrix->set_charlabels( [ 'char1', 'char2', 'char3' ] );
 Function: Assigns character labels.
 Returns : $self
 Args    : ARRAY

ACCESSORS

get_type()
 Type    : Accessor
 Title   : get_type
 Usage   : my $type = $matrix->get_type;
 Function: Retrieves a matrix's type.
 Returns : SCALAR =~ (DNA|RNA|STANDARD|
           PROTEIN|NUCLEOTIDE|CONTINUOUS);
 Args    : NONE
get_symbols()
 Type    : Accessor
 Title   : get_symbols
 Usage   : my $symbols = $matrix->get_symbols;
 Function: Retrieves a matrix's symbol table.
 Returns : ARRAY
 Args    : NONE
get_num_states()
 Type    : Accessor
 Title   : get_num_states
 Usage   : my $nstates = $matrix->get_num_states;
 Function: Retrieves the number of distinct
           states in the matrix
 Returns : SCALAR
 Args    : NONE
get_taxa()
 Type    : Accessor
 Title   : get_taxa
 Usage   : my $taxa = $matrix->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.
get_chars_for_taxon()
 Type    : Accessor
 Title   : get_chars_for_taxon
 Usage   : my @chars = @{
               $matrix->get_chars_for_taxon($taxon)
           };
 Function: Retrieves the datum
           objects for $taxon
 Returns : ARRAY
 Args    : A Bio::Phylo::Taxa::Taxon object
get_cols()
 Type    : Accessor
 Title   : get_cols
 Usage   : my $cols = $matrix->get_cols( 0 .. 100 );
 Function: Retrieves columns in $matrix
 Returns : Bio::Phylo::Matrices::Matrix (shallow copy)
 Args    : Column numbers, zero-based,
           throws exception if out of bounds.
 Notes   : This method can be used as a makeshift
           bootstrapper/jackknifer. The trick is to
           create the appropriate argument list, i.e.
           for bootstrapping one with the same number
           of elements as there are columns in the
           matrix - but resampled with replacement;
           for jackknifing a list where the number
           of elements is that of the number of columns
           to keep. You can generate such a list by
           iteratively calling shift(shuffle(@list))
           where shuffle comes from the List::Util
           package.
get_rows()
 Type    : Accessor
 Title   : get_rows
 Usage   : my $rows = $matrix->get_rows( 0 .. 100 );
 Function: Retrieves rows in $matrix
 Returns : Bio::Phylo::Matrices::Matrix (shallow copy)
 Args    : Row numbers, zero-based, throws
           exception if out of bounds.
 Notes   :
get_charlabels()
 Type    : Accessor
 Title   : get_charlabels
 Usage   : $matrix->get_charlabels;
 Function: Retrieves character labels.
 Returns : ARRAY
 Args    : None.
get_missing()
 Type    : Accessor
 Title   : get_missing
 Usage   : $matrix->get_missing;
 Function: Retrieves the missing data symbol.
 Returns : A single character.
 Args    : None.
get_gap()
 Type    : Accessor
 Title   : get_gap
 Usage   : $matrix->get_gap;
 Function: Retrieves the gap (indel?) character symbol.
 Returns : A single character.
 Args    : None.
get_ntax()
 Type    : Accessor
 Title   : get_ntax
 Usage   : my $ntax = $matrix->get_ntax;
 Function: Retrieves the intended number of
           taxa for the matrix.
 Returns : An integer, or undefined.
 Args    : None.
 Comments: The return value is whatever was
           set by the 'set_ntax' method call.
           'get_ntax' is used by the 'validate'
           method to check if the computed
           number of taxa matches with
           what is asserted here. In other words,
           this method does not return the
           *actual* number of taxa in the matrix
           (use 'get_num_taxa' for that), but the
           number it is supposed to have.
get_nchar()
 Type    : Accessor
 Title   : get_nchar
 Usage   : $matrix->get_nchar;
 Function: Retrieves the intended number of
           characters for the matrix.
 Returns : An integer, or undefined.
 Args    : None.
 Comments: The return value is whatever was
           set by the 'set_nchar' method call.
           'get_nchar' is used by the 'validate'
           method to check if the computed
           number of characters matches with
           what is asserted here.

UTILITY METHODS

copy_atts()
 Type    : Method
 Title   : copy_atts
 Usage   : my $copy = $matrix->copy_atts;
 Function: Creates an empty copy of invocant
           (i.e. no data, but all the attributes).
 Returns : Bio::Phylo::Matrices::Matrix (shallow copy)
 Args    : None
to_nexus()
 Type    : Format convertor
 Title   : to_nexus
 Usage   : my $data_block = $matrix->to_nexus;
 Function: Converts matrix object into a nexus data block.
 Alias   :
 Returns : Nexus data block (SCALAR).
 Args    : none
 Comments:
to_cipres()
 Type    : Format convertor
 Title   : to_cipres
 Usage   : my $cipres_matrix = $matrix->to_cipres;
 Function: Converts matrix object to CipresIDL
 Alias   :
 Returns : CIPRES compliant data structure
 Args    : none
 Comments:
make_taxa()
 Type    : Utility method
 Title   : make_taxa
 Usage   : my $taxa = $matrix->make_taxa;
 Function: Creates a Bio::Phylo::Taxa object
           from the data in invocant.
 Returns : Bio::Phylo::Taxa
 Args    : NONE
 Comments: NOTE: the newly created taxa
           object will replace all earlier
           references to other taxa and
           taxon objects.

DESTRUCTOR

DESTROY()
 Type    : Destructor
 Title   : DESTROY
 Usage   : $phylo->DESTROY
 Function: Destroys Phylo object
 Alias   :
 Returns : TRUE
 Args    : none
 Comments: You don't really need this,
           it is called automatically when
           the object goes out of scope.

Re-Implemented Bio::Matrix::MatrixI methods

Consult the Bio::Matrix::MatrixI documentation for details about the following methods:

matrix_id()
matrix_name()
num_rows()
num_columns()
row_names()
column_names()
column_num_for_name()

SEE ALSO

Bio::CDAT::CharMatrixI

This object implements the Bio::CDAT::CharMatrixI interface, so the methods defined therein are available here.

Bio::Phylo::Listable

This object inherits from Bio::Phylo::Listable, so the methods defined therein are also applicable to Bio::Phylo::Matrices::Matrix 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: Matrix.pm 2187 2006-09-07 07:13:33Z 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.