Bio::Matrix::Generic(3pm)				User Contributed Perl Documentation				 Bio::Matrix::Generic(3pm)

NAME

       Bio::Matrix::Generic - A generic matrix implementation

SYNOPSIS

	 # A matrix has columns and rows
	 my $matrix = Bio::Matrix::Generic->new;
	 $matrix->add_column(1,$column1);
	 $matrix->add_column(2,$column2);

	 my $element = $matrix->entry_by_num(1,2);
	 $matrix->entry_by_num(1,2,$newval);

	 my $entry = $matrix->entry('human', 'mouse');

	 $matrix->entry('human','mouse', $newval);

DESCRIPTION

       This is a general purpose matrix object for dealing with row+column data which is typical when enumerating all the pairwise combinations
       and desiring to get slices of the data.

       Data can be accessed by column and row names or indexes.  Matrix indexes start at 0.

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 the
       Bioperl mailing list.  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 of the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich
       Email 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 $obj = Bio::Matrix::Generic->new();
	Function: Builds a new Bio::Matrix::Generic object
	Returns : an instance of Bio::Matrix::Generic
	Args	: -values     => arrayref of arrayrefs of data initialization
		  -rownames   => arrayref of row names
		  -colnames   => arrayref of col names
		  -matrix_id  => id of the matrix
		  -matrix_name=> name of the matrix
		  -matrix_init_value => default value to initialize empty cells

   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

   entry
	Title	: entry
	Usage	: my $entry = $matrix->entry($row,$col)
	Function: Get the value for a specific cell as specified
		  by the row and column names
	Returns : scalar value or undef if row or col does not
		  exist
	Args	: $rowname - name of the row
		  $colname - column name

   get_entry
	Title	: get_entry
	Usage	: my $entry = $matrix->get_entry($rowname,$columname)
	Function: Get the entry for a given row,column pair
	Returns : scalar
	Args	: $row name
		  $column name

   entry_by_num
	Title	: entry_by_num
	Usage	: my $entry = $matrix->entry_by_num($rownum,$colnum)
	Function: Get an entry by row and column numbers instead of by name
		  (rows and columns start at 0)
	Returns : scalar value or undef if row or column name does not
		  exist
	Args	: $row - row number
		  $col - column number
		  [optional] $newvalue to store at this cell

   column
	Title	: column
	Usage	: my @col = $matrix->column('ALPHA');
		  OR
		  $matrix->column('ALPHA', @col);
	Function: Get/Set a particular column
	Returns : Array (in array context) or arrayref (in scalar context)
		  of values.
		  For setting will warn if the new column is of a different
		  length from the rest of the columns.
	Args	: name of the column
		  [optional] new column to store here

   get_column
	Title	: get_column
	Usage	: my @row = $matrix->get_column('ALPHA');
	Function: Get a particular column
	Returns : Array (in array context) or arrayref (in scalar context)
		  of values
	Args	: name of the column

   column_by_num
	Title	: column_by_num
	Usage	: my @col = $matrix->column_by_num(1);
		  OR
		  $matrix->column_by_num(1,@newcol);
	Function: Get/Set a column by its number instead of name
		  (cols/rows start at 0)
	Returns : Array (in array context) or arrayref (in scalar context)
		  of values
	Args	: name of the column
		  [optional] new value to store for a particular column

   row
	Title	: row
	Usage	: my @row = $matrix->row($rowname);
		    OR
		  $matrix->row($rowname,@rowvalues);
	Function: Get/Set the row of the matrix
	Returns : Array (in array context) or arrayref (in scalar context)
	Args	: rowname
		  [optional] new value of row to store

   get_row
	Title	: get_row
	Usage	: my @row = $matrix->get_row('ALPHA');
	Function: Get a particular row
	Returns : Array (in array context) or arrayref (in scalar context)
		  of values
	Args	: name of the row

   row_by_num
	Title	: row_by_num
	Usage	: my @row = $matrix->row_by_num($rownum);
		    OR
		  $matrix->row($rownum,@rowvalues);
	Function: Get/Set the row of the matrix
	Returns : Array (in array context) or arrayref (in scalar context)
	Args	: rowname
		  [optional] new value of row to store

   diagonal
	Title	: diagonal
	Usage	: my @diagonal = $matrix->get_diagonal()
	Function: Get the diagonal of a matrix
	Returns : Array (in array context) or arrayref (in scalar context)
		  of values which lie along the diagonal
	Args	: none

   add_row
	Title	: add_row
	Usage	: $matrix->add_row($index,@newrow);
	Function: Adds a row at particular location in the matrix.
		  If $index < the rowcount will shift all the rows down
		  by the number of new rows.
		  To add a single empty row, simply call
		  $matrix->add_row($index,undef);
	Returns : the updated number of total rows in the matrix
	Args	: index to store
		  name of the row (header)
		  newrow to add, if this is undef will add a single
			    row with all values set to undef

   remove_row
	Title	: remove_row
	Usage	: $matrix->remove_row($colnum)
	Function: remove a row from the matrix shifting all the rows
		  up by one
	Returns : Updated number of rows in the matrix
	Args	: row index

   add_column
	Title	: add_column
	Usage	: $matrix->add_column($index,$colname,@newcol);
	Function: Adds a column at particular location in the matrix.
		  If $index < the colcount will shift all the columns right
		  by the number of new columns.
		  To add a single empty column, simply call
		  $matrix->add_column($index,undef);
	Returns : the updated number of total columns in the matrix
	Args	: index to store
		  name of the column (header)
		  newcolumn to add, if this is undef will add a single
			column with all values set to undef

   remove_column
	Title	: remove_column
	Usage	: $matrix->remove_column($colnum)
	Function: remove a column from the matrix shifting all the columns
		  to the left by one
	Returns : Updated number of columns in the matrix
	Args	: column index

   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
	Function: Gets the row number for a particular row name
	Returns : integer
	Args	: string

   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

   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

   private methods
       Private methods for a Generic Matrix

   _values
	Title	: _values
	Usage	: $matrix->_values();
	Function: get/set for array ref of the matrix containing
		  distance values
	Returns : an array reference
	Args	: an array reference

perl v5.14.2							    2012-03-02						 Bio::Matrix::Generic(3pm)