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://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
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