Bio::Matrix::PhylipDist(3)

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:

  http://bugzilla.open-bio.org/

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