/ 
bioperl-1.2.2
/ Bio::Matrix::PhylipDist

NAME

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

SYNOPSIS

use Bio::Matrix::PhylipDist;

my $dist = Bio::Matrix::PhylipDist->new(-file=>"protdist.out",-program=>"ProtDist");
#or
my $dist = Bio::Matrix::PhylipDist->new(-fh=>$FH,-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://bio.perl.org/MailList.html  - About the mailing lists

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 email or the web:

bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/

AUTHOR - Shawn Hoon

Email shawnh@fugu-sg.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>

_parse

Title   : _parse
Usage   : $matrix->_parse();
Function: internal method that parses the distance matrix file. 
Returns : 
Arguments:

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
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