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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:

   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