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)