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

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq