GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages


Manual Reference Pages  -  BIO::MATRIX::GENERIC (3)

.ds Aq ’

NAME

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

CONTENTS

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



Search for    or go to Top of page |  Section 3 |  Main Index


perl v5.20.3 BIO::MATRIX::GENERIC (3) 2016-04-05

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with manServer 1.07.