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.\" ========================================================================
.\"
.IX Title "Bio::PhyloNetwork::muVector 3pm"
.TH Bio::PhyloNetwork::muVector 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::PhyloNetwork::muVector \- Module to compute with vectors of arbitrary
dimension
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\& 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\en";
\& }
\&
\& 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)."\en";
\& print "Test lex $vec5 > $vec6: ".($vec5 cmp $vec6)."\en";
.Ve
.SH "DESCRIPTION"
.IX Header "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.
.SH "AUTHOR"
.IX Header "AUTHOR"
Gabriel Cardona, gabriel(dot)cardona(at)uib(dot)es
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
.SS "new"
.IX Subsection "new"
.Vb 5
\& 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
.Ve
.PP
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.
.SS "display"
.IX Subsection "display"
.Vb 5
\& Title   : display
\& Usage   : my $str=$mu\->display()
\& Function: returns an string displaying its contents
\& Returns : string
\& Args    : none
.Ve
.PP
This function is also overloaded to the "" operator.
.SS "add"
.IX Subsection "add"
.Vb 5
\& Title   : add
\& Usage   : $mu\->add($mu2)
\& Function: returns the sum of $mu and $mu2
\& Returns : Bio::PhyloNetwork::muVector
\& Args    : Bio::PhyloNetwork::muVector
.Ve
.PP
This function is also overloaded to the + operator.
.SS "substract"
.IX Subsection "substract"
.Vb 5
\& Title   : substract
\& Usage   : $mu\->substract($mu2)
\& Function: returns the difference of $mu and $mu2
\& Returns : Bio::PhyloNetwork::muVector
\& Args    : Bio::PhyloNetwork::muVector
.Ve
.PP
This function is also overloaded to the \- operator.
.SS "scalarproduct"
.IX Subsection "scalarproduct"
.Vb 5
\& Title   : scalarproduct
\& Usage   : $mu\->scalarproduct($ct)
\& Function: returns the scalar product of $ct and $mu
\& Returns : Bio::PhyloNetwork::muVector
\& Args    : scalar
.Ve
.PP
This function is also overloaded to the * operator.
.SS "comparelex"
.IX Subsection "comparelex"
.Vb 5
\& 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
.Ve
.PP
This function is also overloaded to the <=> and cmp operator.
.SS "geq_poset"
.IX Subsection "geq_poset"
.Vb 5
\& 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
.Ve
.SS "is_positive"
.IX Subsection "is_positive"
.Vb 5
\& Title   : is_positive
\& Usage   : $mu\->is_positive()
\& Function: tests if all components of $mu are positive (or zero)
\& Returns : boolean
\& Args    : none
.Ve
.SS "hamming"
.IX Subsection "hamming"
.Vb 5
\& Title   : hamming
\& Usage   : $mu1\->hamming($mu2)
\& Function: returns the Hamming distance between $mu1 and $mu2
\& Returns : scalar
\& Args    : Bio::PhyloNetwork::muVector
.Ve
.SS "manhattan"
.IX Subsection "manhattan"
.Vb 5
\& Title   : manhattan
\& Usage   : $mu1\->manhattan($mu2)
\& Function: returns the Manhattan distance between $mu1 and $mu2
\& Returns : scalar
\& Args    : Bio::PhyloNetwork::muVector
.Ve