Provided by: libbio-perl-perl_1.7.2-3_all bug

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

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].