Bio::Matrix::Generic(3)

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://github.com/bioperl/bioperl-live/issues

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