Bio::Matrix::PhylipDist(3pm)				User Contributed Perl Documentation			      Bio::Matrix::PhylipDist(3pm)

NAME

       Bio::Matrix::PhylipDist - A Phylip Distance Matrix object

SYNOPSIS

	 use Bio::Tools::Phylo::Phylip::ProtDist;
	 my $dist = Bio::Tools::Phylo::Phylip::ProtDist->new(
	   -file=>"protdist.out",
	   -program=>"ProtDist");
	 #or
	  my $dist = Bio::Tools::Phylo::Phylip::ProtDist->new(
	   -fh=>"protdist.out",
	   -program=>"ProtDist");

	 #get specific entries
	 my $distance_value = $dist->get_entry('ALPHA','BETA');
	 my @columns	    = $dist->get_column('ALPHA');
	 my @rows	    = $dist->get_row('BETA');
	 my @diagonal	    = $dist->get_diagonal();

	 #print the matrix in phylip numerical format
	 print $dist->print_matrix;

DESCRIPTION

       Simple object for holding Distance Matrices generated by the following Phylip programs:

       1) dnadist 2) protdist 3) restdist

       It currently handles parsing of the matrix without the data output option.

	   5
       Alpha	      0.00000  4.23419	3.63330  6.20865  3.45431
       Beta	      4.23419  0.00000	3.49289  3.36540  4.29179
       Gamma	      3.63330  3.49289	0.00000  3.68733  5.84929
       Delta	      6.20865  3.36540	3.68733  0.00000  4.43345
       Epsilon	      3.45431  4.29179	5.84929  4.43345  0.00000

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one
       of the Bioperl mailing lists. Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution.  Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Shawn Hoon
       Email shawnh@fugu-sg.org

CONTRIBUTORS

       Jason Stajich, jason-at-bioperl-dot-org

APPENDIX

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

   new
	Title	: new
	Usage	: my $family = Bio::Matrix::PhylipDist->new(-file=>"protdist.out",
							    -program=>"protdist");
	Function: Constructor for PhylipDist Object
	Returns : L<Bio::Matrix::PhylipDist>

   get_entry
	Title	: get_entry
	Usage	: $matrix->get_entry();
	Function: returns a particular entry
	Returns : a float
	Arguments:  string id1, string id2

   get_row
	Title	: get_row
	Usage	: $matrix->get_row('ALPHA');
	Function: returns a particular row
	Returns : an array of float
	Arguments:  string id1

   get_column
	Title	: get_column
	Usage	: $matrix->get_column('ALPHA');
	Function: returns a particular column
	Returns : an array of floats
	Arguments:  string id1

   get_diagonal
	Title	: get_diagonal
	Usage	: $matrix->get_diagonal();
	Function: returns the diagonal of the matrix
	Returns : an array of float
	Arguments:  string id1

   print_matrix
	Title	: print_matrix
	Usage	: $matrix->print_matrix();
	Function: returns a string of the matrix in phylip format
	Returns : a string
	Arguments:

   _matrix
	Title	: _matrix
	Usage	: $matrix->_matrix();
	Function: get/set for hash reference of the pointers
		  to the value matrix
	Returns : hash reference
	Arguments: hash reference

   names
	Title	: names
	Usage	: $matrix->names();
	Function: get/set for array ref of names of sequences
	Returns : an array reference
	Arguments: an array reference

   program
	Title	: program
	Usage	: $matrix->program();
	Function: get/set for the program name generating this
		  matrix
	Returns : string
	Arguments: string

   _values
	Title	: _values
	Usage	: $matrix->_values();
	Function: get/set for array ref of the matrix containing
		  distance values
	Returns : an array reference
	Arguments: an array reference

Bio::Matrix::MatrixI implementation
   matrix_id
	Title	: matrix_id
	Usage	: my $id = $matrix->matrix_id
	Function: Get/Set the matrix ID
	Returns : scalar value
	Args	: [optional] new id value to store

   matrix_name
	Title	: matrix_name
	Usage	: my $name = $matrix->matrix_name();
	Function: Get/Set the matrix name
	Returns : scalar value
	Args	: [optional] new matrix name value

   column_header
	Title	: column_header
	Usage	: my $name = $matrix->column_header(0)
	Function: Gets the column header for a particular column number
	Returns : string
	Args	: integer

   row_header
	Title	: row_header
	Usage	: my $name = $matrix->row_header(0)
	Function: Gets the row header for a particular row number
	Returns : string
	Args	: integer

   column_num_for_name
	Title	: column_num_for_name
	Usage	: my $num = $matrix->column_num_for_name($name)
	Function: Gets the column number for a particular column name
	Returns : integer
	Args	: string

   row_num_for_name
	Title	: row_num_for_name
	Usage	: my $num = $matrix->row_num_for_name($name)
	Function: Gets the row number for a particular row name
	Returns : integer
	Args	: string

   num_rows
	Title	: num_rows
	Usage	: my $rowcount = $matrix->num_rows;
	Function: Get the number of rows
	Returns : integer
	Args	: none

   num_columns
	Title	: num_columns
	Usage	: my $colcount = $matrix->num_columns
	Function: Get the number of columns
	Returns : integer
	Args	: none

   row_names
	Title	: row_names
	Usage	: my @rows = $matrix->row_names
	Function: The names of all the rows
	Returns : array in array context, arrayref in scalar context
	Args	: none

   column_names
	Title	: column_names
	Usage	: my @columns = $matrix->column_names
	Function: The names of all the columns
	Returns : array in array context, arrayref in scalar context
	Args	: none

perl v5.14.2							    2012-03-02					      Bio::Matrix::PhylipDist(3pm)