Bio::Matrix::PhylipDist

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 AT bioperl DOT 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 AT bioperl DOT 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://github.com/bioperl/bioperl-live/issues

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