bio::phylonetwork::graphviz(3pm) [debian man page]
Bio::PhyloNetwork::GraphViz(3pm) User Contributed Perl Documentation Bio::PhyloNetwork::GraphViz(3pm) NAME
Bio::PhyloNetwork::GraphViz - Interface between PhyloNetwork and GraphViz SYNOPSIS
use Bio::PhyloNetwork; use Bio::PhyloNetwork::GraphViz; my $net=Bio::PhyloNetwork->new( -eNewick=>'((H1,(H1,(H2,l))),H2)t0; (some long label)H1; ("quoted label")H2;' ); my $gv=Bio::PhyloNetwork::GraphViz->new(-net=>$net,-short_labels=>1); foreach my $u ($net->nodes()) { print "$u:".$gv->nodePN_to_nodeGV->{$u}." "; } print $gv->as_text; open PS, "> net.ps"; print PS $gv->as_ps; close PS; DESCRIPTION
This is a module to create GraphViz objects representing phylogenetic networks. AUTHOR
Gabriel Cardona, gabriel(dot)cardona(at)uib(dot)es SEE ALSO
Bio::PhyloNetwork, GraphViz APPENDIX
The rest of the documentation details each of the object methods. new Title : new Usage : my $graphv = new Bio::PhyloNetwork::GraphViz(); Function: Creates a new Bio::PhyloNetwork::GraphViz object Returns : Bio::PhyloNetwork::GraphViz Args : -net => Bio::PhyloNetwork object -short_labels => boolean (optional) Returns a Bio::PhyloNetwork::GraphViz object, which is an extension of a GraphViz object. The GraphViz object is a representation of the phylogenetic network given. The extra information the created object holds is a hash table with keys the nodes of the PhyloNetwork object and values the nodes of the GraphViz object. If the optional argument -short_labels=>1 is given, the labels of the nodes in GraphViz are shortened to a maximum of 3 letters. nodePN_to_nodeGV Title : nodePN_to_nodeGV Usage : my $hashR=$graphv->nodePN_to_nodeGV() Function: returns (a reference to) a hash holding the translation between nodes of the Bio::PhyloNetwork object and nodes of the GraphViz object Returns : reference to hash Args : none perl v5.14.2 2012-03-02 Bio::PhyloNetwork::GraphViz(3pm)
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Bio::PhyloNetwork::muVector(3pm) User Contributed Perl Documentation Bio::PhyloNetwork::muVector(3pm) 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 "; } 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)." "; print "Test lex $vec5 > $vec6: ".($vec5 cmp $vec6)." "; 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 perl v5.14.2 2012-03-02 Bio::PhyloNetwork::muVector(3pm)