Bio::PhyloNetwork::muVector.3pm

Langue: en

Version: 2009-03-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::PhyloNetwork::muVector - Module to compute with vectors of arbitrary dimension

SYNOPSIS

  use strict;
  use warnings;
 
  use Bio::PhyloNetwork::muVector;
 
  my $vec1=Bio::PhyloNetwork::muVector->new(4);
  my $vec2=Bio::PhyloNetwork::muVector->new([1,2,3,4]);
  my $vec3=Bio::PhyloNetwork::muVector->new([10,20,30,40]);
 
  my $vec4=$vec3-10*$vec2;
  if (($vec4 cmp $vec1) == 0) {
    print "$vec4 is zero\n";
  }
 
  my $vec5=Bio::PhyloNetwork::muVector->new([8,2,2,4]);
  my $vec6=Bio::PhyloNetwork::muVector->new([1,2,3,4]);
 
  print "Test poset $vec5 > $vec6: ".$vec5->geq_poset($vec6)."\n";
  print "Test lex $vec5 > $vec6: ".($vec5 cmp $vec6)."\n";
 
 

DESCRIPTION

This is a module to work with vectors. It creates vectors of arbitrary length, defines its basic arithmetic operations, its lexicographic ordering and the natural structure of poset.

AUTHOR

Gabriel Cardona, gabriel(dot)cardona(at)uib(dot)es

APPENDIX

The rest of the documentation details each of the object methods.

new

  Title   : new
  Usage   : my $mu = new Bio::PhyloNetwork::muVector();
  Function: Creates a new Bio::PhyloNetwork::muVector object
  Returns : Bio::PhyloNetwork::muVector
  Args    : integer or (reference to) an array
 
 

If given an integer as argument, returns a Bio::PhyloNetwork::muVector object with dimension the integer given and initialized to zero. If it is an anonimous array, then the vector is initialized with the values in the array and with the corresponding dimension.

display

  Title   : display
  Usage   : my $str=$mu->display()
  Function: returns an string displaying its contents
  Returns : string
  Args    : none
 
 

This function is also overloaded to the "" operator.

add

  Title   : add
  Usage   : $mu->add($mu2)
  Function: returns the sum of $mu and $mu2
  Returns : Bio::PhyloNetwork::muVector
  Args    : Bio::PhyloNetwork::muVector
 
 

This function is also overloaded to the + operator.

substract

  Title   : substract
  Usage   : $mu->substract($mu2)
  Function: returns the difference of $mu and $mu2
  Returns : Bio::PhyloNetwork::muVector
  Args    : Bio::PhyloNetwork::muVector
 
 

This function is also overloaded to the - operator.

scalarproduct

  Title   : scalarproduct
  Usage   : $mu->scalarproduct($ct)
  Function: returns the scalar product of $ct and $mu
  Returns : Bio::PhyloNetwork::muVector
  Args    : scalar
 
 

This function is also overloaded to the * operator.

comparelex

  Title   : comparelex
  Usage   : $mu1->comparelex($mu2)
  Function: compares $mu and $mu2 w.r.t. the lexicographic ordering
  Returns : scalar (-1 if $mu1<$mu2, 0 if $mu1=$mu2, 1 if $mu1>$mu2)
  Args    : Bio::PhyloNetwork::muVector
 
 

This function is also overloaded to the <=> and cmp operator.

geq_poset

  Title   : geq_poset
  Usage   : $mu1->geq_poset($mu2)
  Function: compares $mu and $mu2 w.r.t. the natural partial ordering
  Returns : boolean (1 if $mu >= $mu2, 0 otherwise)
  Args    : Bio::PhyloNetwork::muVector
 
 

is_positive

  Title   : is_positive
  Usage   : $mu->is_positive()
  Function: tests if all components of $mu are positive (or zero)
  Returns : boolean
  Args    : none
 
 

hamming

  Title   : hamming
  Usage   : $mu1->hamming($mu2)
  Function: returns the Hamming distance between $mu1 and $mu2
  Returns : scalar
  Args    : Bio::PhyloNetwork::muVector
 
 

manhattan

  Title   : manhattan
  Usage   : $mu1->manhattan($mu2)
  Function: returns the Manhattan distance between $mu1 and $mu2
  Returns : scalar
  Args    : Bio::PhyloNetwork::muVector