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Man Pages


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

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NAME

Bio::Phylo::Matrices::Matrix - Character state matrix

CONTENTS

SYNOPSIS



 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;



DESCRIPTION

This module defines a container object that holds Bio::Phylo::Matrices::Datum objects. The matrix object inherits from Bio::Phylo::MatrixRole, so the methods defined there apply here.

METHODS

    MUTATORS

set_statelabels() 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 whats appropriate)



set_characters() Sets the character set manager object Bio::Phylo::Matrices::Characters. Normally you never have to use this.



 Type    : Mutator
 Title   : set_characters
 Usage   : $matrix->set_characters( $characters );
 Function: Assigns Bio::Phylo::Matrices::Characters object
 Returns : $self
 Args    : Bio::Phylo::Matrices::Characters



set_gapmode() 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



set_matchchar() Assigns match symbol.



 Type    : Mutator
 Title   : set_matchchar
 Usage   : $matrix->set_matchchar( $match );
 Function: Assigns match symbol (default is .).
 Returns : $self
 Args    : ARRAY



set_polymorphism() 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_respectcase() 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



    ACCESSORS

get_characters() Retrieves characters object.



 Type    : Accessor
 Title   : get_characters
 Usage   : my $characters = $matrix->get_characters
 Function: Retrieves characters object.
 Returns : Bio::Phylo::Matrices::Characters
 Args    : None.



get_statelabels() Retrieves state labels.



 Type    : Accessor
 Title   : get_statelabels
 Usage   : my @statelabels = @{ $matrix->get_statelabels };
 Function: Retrieves state labels.
 Returns : ARRAY
 Args    : None.



get_gapmode() 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



get_matchchar() 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



get_polymorphism() 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



get_respectcase() 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



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::Taxa::TaxaLinker This object inherits from Bio::Phylo::Taxa::TaxaLinker, so the methods defined therein are also applicable to Bio::Phylo::Matrices::Matrix objects.
Bio::Phylo::Matrices::TypeSafeData This object inherits from Bio::Phylo::Matrices::TypeSafeData, so the methods defined therein are also applicable to Bio::Phylo::Matrices::Matrix 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>

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