Bio::Matrix::PhylipDist - A Phylip Distance Matrix object 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; 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

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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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ Email shawnh@fugu-sg.org Jason Stajich, jason-at-bioperl-dot-org 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

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

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