Bio::Matrix::MatrixI.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Matrix::MatrixI - An interface for describing a Matrix

SYNOPSIS

   # Get a Matrix object
 
 

DESCRIPTION

This is an interface describing how one should be able to interact with a matrix. One can have a lot of information I suppose and this outline won't really work for PWM or PSSMs. We will have to derive a particular interface for those.

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 email or the web:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Jason Stajich

Email jason-at-bioperl.org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

matrix_id

  Title   : matrix_id
  Usage   : my $id = $matrix->matrix_id
  Function: Get the matrix ID
  Returns : string value
  Args    :
 
 

matrix_name

  Title   : matrix_name
  Usage   : my $name = $matrix->matrix_name();
  Function: Get the matrix name
  Returns : string value
  Args    :
 
 

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
 
 

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
 
 

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
 
 

get_diagonal

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

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
 
 

reverse

  Title   : reverse
  Usage   : my $matrix = $matrix->reverse
  Function: Get the reverse of a matrix
  Returns : 
  Args    :
 
 

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