| 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://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
| 2021-08-15 | perl v5.32.1 |