bio::phylonetwork::muvector(3pm) [debian man page]

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)

Check Out this Related Man Page

Bio::Annotation::Comment(3pm)				User Contributed Perl Documentation			     Bio::Annotation::Comment(3pm)

NAME

       Bio::Annotation::Comment - A comment object, holding text

SYNOPSIS

	   $comment = Bio::Annotation::Comment->new();
	   $comment->text("This is the text of this comment");
	   $annotation->add_Annotation('comment', $comment);

DESCRIPTION

       A holder for comments in annotations, just plain text. This is a very simple object, and justifiably so.

AUTHOR - Ewan Birney
       Email birney@ebi.ac.uk

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

   new
	Title	: new
	Usage	: $comment = Bio::Annotation::Comment->new( '-text' => 'some text for this comment');
	Function: This returns a new comment object, optionally with
		  text filed
	Example :
	Returns : a Bio::Annotation::Comment object
	Args	: a hash with -text optionally set

AnnotationI implementing functions
   as_text
	Title	: as_text
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   display_text
	Title	: display_text
	Usage	: my $str = $ann->display_text();
	Function: returns a string. Unlike as_text(), this method returns a string
		  formatted as would be expected for te specific implementation.

		  One can pass a callback as an argument which allows custom text
		  generation; the callback is passed the current instance and any text
		  returned
	Example :
	Returns : a string
	Args	: [optional] callback

   hash_tree
	Title	: hash_tree
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   tagname
	Title	: tagname
	Usage	: $obj->tagname($newval)
	Function: Get/set the tagname for this annotation value.

		  Setting this is optional. If set, it obviates the need to
		  provide a tag to Bio::AnnotationCollectionI when adding
		  this object. When obtaining an AnnotationI object from the
		  collection, the collection will set the value to the tag
		  under which it was stored unless the object has a tag
		  stored already.

	Example :
	Returns : value of tagname (a scalar)
	Args	: new value (a scalar, optional)

Specific accessors for Comments
   text
	Title	: text
	Usage	: $value = $self->text($newval)
	Function: get/set for the text field. A comment object
		  just holds a single string which is accessible through
		  this method
	Example :
	Returns : value of text
	Args	: newvalue (optional)

   value
	Title	: value
	Usage	: $value = $self->value($newval)
	Function: Alias of the 'text' method
	Example :
	Returns : value of text
	Args	: newvalue (optional)

   type
	Title	: type
	Usage	: $value = $self->type($newval)
	Function: get/set for the comment type field.  The comment type
		  is normally found as a subfield within comment sections
		  in some files, such as SwissProt
	Example :
	Returns : value of text
	Args	: newvalue (optional)

perl v5.14.2							    2012-03-02					     Bio::Annotation::Comment(3pm)

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bio::phylonetwork::muvector(3pm) [debian man page]

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