Bio::Matrix::GenericMatrix - A generic matrix implementation # A matrix has columns and rows my $matrix = new Bio::Matrix::GenericMatrix(); $matrix->add_column_num(1,$column1); $matrix->add_column_num(2,$column2); my $element = $matrix->element(1,2); $matrix->element(1,2,$newval); my $entry = $matrix->entry('human', 'mouse'); $matrix->entry('human','mouse', $newval); 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 1.

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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: http://bugzilla.bioperl.org/ Email jason-at-bioperl-dot-org Describe contact details here Additional contributors names and emails here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $obj = new Bio::Matrix::Generic(); Function: Builds a new Bio::Matrix::Generic object Returns : an instance of Bio::Matrix::Generic Args :

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_name Usage : my $entry = $matrix->entry_by_name($rowname,$colname) 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