Bio::Tools::ECnumber(3pm)				User Contributed Perl Documentation				 Bio::Tools::ECnumber(3pm)

NAME

       Bio::Tools::ECnumber - representation of EC numbers (Enzyme Classification)

SYNOPSIS

	 use Bio::Tools::ECnumber;

	 # Creation of ECnumber objects
	 my $EC1 = Bio::Tools::ECnumber->new( -ec_string => "4.3.2.1" );
	 my $EC2 = Bio::Tools::ECnumber->new( -ec_string => "EC 1.1.1.1" );
	 my $EC3 = Bio::Tools::ECnumber->new();

	 # Copying
	 my $EC4 = $EC1->copy();

	 # Modification/canonicalization of ECnumber objects
	 print $EC3->EC_string( "1.01.01.001" ); # Prints "1.1.1.1".

	 # Stringify
	 print $EC3->EC_string();
	 # or
	 print $EC3->to_string();

	 # Test for equality
	 # -- Against ECnumber object:
	 if ( $EC3->is_equal( $EC2 ) ) { # Prints "equal".
	     print "equal";
	 }
	 # -- Against string representation of EC number:
	 if ( ! $EC3->is_equal( "1.1.1.-" ) ) { # Prints "not equal".
	     print "not equal";
	 }

	 # Test for membership
	 my $EC5 = Bio::Tools::ECnumber->new( -ec_string => "4.3.2.-" );
	 # -- Against ECnumber object.
	 if ( $EC1->is_member( $EC5 ) ) { # Prints "member".
	     print "member";
	 }
	 # -- Against string representation of EC number.
	 if ( ! $EC1->is_member( "4.3.1.-" ) ) { # Prints "not member".
	     print "not member";
	 }

DESCRIPTION

       Bio::Tools::ECnumber is a representation of EC numbers, the numerical heirarchy for Enzyme Classification.

       See <http://www.chem.qmul.ac.uk/iubmb/enzyme/> for more details.

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

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

AUTHOR

       Christian M. Zmasek

       Email: czmasek-at-burnham.org  or  cmzmasek@yahoo.com

       WWW:   http://monochrome-effect.net/

       Address:

	 Genomics Institute of the Novartis Research Foundation
	 10675 John Jay Hopkins Drive
	 San Diego, CA 92121

APPENDIX

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

   new
	Title	: new
	Usage	: $EC1 = Bio::Tools::ECnumber->new( -ec_string => "4.3.2.1" );
		  or
		  $EC2 = Bio::Tools::ECnumber->new( -ec_string => "4.3.2.2",
						    -comment   => "Is EC 4.3.2.2" );
		  or
		  $EC3 = Bio::Tools::ECnumber->new(); # EC3 is now "-.-.-.-"
	Function: Creates a new ECnumber object.
		  Parses a EC number from "x.x.x.x", "EC x.x.x.x",
		  "ECx.x.x.x", or "EC:x.x.x.x";
		  x being either a positive integer or a "-".
	Returns : A new ECnumber object.
	Args	: A string representing a EC number, e.g. "4.3.2.1"
		  or "EC 4.3.2.1" or "1.-.-.-".

   init
	Title	: init()
	Usage	: $EC1->init(); # EC1 is now "-.-.-.-"
	Function: Initializes this ECnumber to default values.
	Returns :
	Args	:

   copy
	Title	: copy()
	Usage	: $EC2 = $EC1->copy();
	Function: Creates a new ECnumber object which is an exact copy
		  of this ECnumber.
	Returns : A copy of this ECnumber.
	Args	:

   EC_string
	Title	: EC_string
	Usage	: $EC3->EC_string( "1.1.1.-" );
		  or
		  print $EC3->EC_string();
	Function: Set/get for string representations of EC numbers.
		  Parses a EC number from "x.x.x.x", "EC x.x.x.x",
		  "ECx.x.x.x", or "EC:x.x.x.x";
		  x being either a positive integer or a "-".
	Returns : A string representations of a EC number.
	Args	: A string representations of a EC number.

   to_string
	Title	: to_string()
	Usage	: print $EC3->to_string();
	Function: To string method for EC numbers
		  (equals the "get" functionality of "EC_string").
	Returns : A string representations of a EC number.
	Args	:

   is_equal
	Title	: is_equal
	Usage	: if ( $EC3->is_equal( $EC2 ) )
		  or
		  if ( $EC3->is_equal( "1.1.1.-" ) )
	Function: Checks whether this ECnumber is equal to the argument
		  EC number (please note: "1.1.1.1" != "1.1.1.-").
	Returns : True(1) or false(0).
	Args	: A ECnumber object or a string representation of a EC number.

   is_member
	Title	: is_member
	Usage	: if ( $EC1->is_member( $EC5 ) )
		  or
		  if ( $EC1->is_member( "4.3.-.-" ) )
	Function: Checks whether this ECnumber is a member of the (incomplete)
		  argument EC number (e.g. "1.1.1.1" is a member of "1.1.1.-"
		  but not of "1.1.1.2").
	Returns : True(1) or false(0).
	Args	: A ECnumber object or a string representation of a EC number.

   enzyme_class
	Title	: enzyme_class
	Usage	: $EC1->enzyme_class( 1 );
		  or
		  print $EC1->enzyme_class();
	Function: Set/get for the enzyme class number of ECnumbers.
	Returns : The enzyme class number of this ECnumber.
	Args	: A positive integer or "-".

   sub_class
	Title	: sub_class
	Usage	: $EC1->sub_class( 4 );
		  or
		  print $EC1->sub_class();
	Function: Set/get for the enzyme sub class number of ECnumbers.
	Returns : The enzyme sub class number of this ECnumber.
	Args	: A positive integer or "-".

   sub_sub_class
	Title	: sub_sub_class
	Usage	: $EC1->sub_sub_class( 12 );
		  or
		  print $EC1->sub_sub_class();
	Function: Set/get for the enzyme sub sub class number of ECnumbers.
	Returns : The enzyme sub sub class number of this ECnumber.
	Args	: A positive integer or "-".

   serial_number
	Title	: serial_number
	Usage	: $EC1->serial_number( 482 );
		  or
		  print $EC1->serial_number();
	Function: Set/get for the serial number of ECnumbers.
	Returns : The serial number of this ECnumber.
	Args	: A positive integer or "-".

   comment
	Title	: comment
	Usage	: $EC1->comment( "deprecated" );
		  or
		  print $EC1->comment();
	Function: Set/get for a arbitrary comment.
	Returns : A comment [scalar].
	Args	: A comment [scalar].

perl v5.14.2							    2012-03-02						 Bio::Tools::ECnumber(3pm)