--- name: "Bio::Matrix::PhylipDist" section: "3pm" platform: "linux" package: "libbio-perl-perl" version: "1.7.8-1" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/Bio::Matrix::PhylipDist" --- # Bio::Matrix::PhylipDist(3pm) A Phylip Distance Matrix object ## 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 ``` ### 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 ```