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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list: [email protected] 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 [email protected]

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