#
# BioPerl module for Bio::Tools::ECnumber
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Christian M. Zmasek <czmasek-at-burnham.org> or <cmzmasek@yahoo.com>
#
# (c) Christian M. Zmasek, czmasek-at-burnham.org, 2002.
# (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
#
# You may distribute this module under the same terms as perl itself.
# Refer to the Perl Artistic License (see the license accompanying this
# software package, or see http://www.perl.com/language/misc/Artistic.html)
# for the terms under which you may use, modify, and redistribute this module.
#
# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
#
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::ECnumber - representation of EC numbers (Enzyme Classification)
=head1 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";
}
=head1 DESCRIPTION
L<Bio::Tools::ECnumber> is a representation of EC numbers,
the numerical heirarchy for Enzyme Classification.
See L<http://www.chem.qmul.ac.uk/iubmb/enzyme/> for more details.
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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/
=head1 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
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Tools::ECnumber;
use strict;
use constant DEFAULT => "-";
use constant TRUE => 1;
use constant FALSE => 0;
use base qw(Bio::Root::Root);
=head2 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.-.-.-".
=cut
sub new {
my( $class, @args ) = @_;
my $self = $class->SUPER::new( @args );
my ( $EC_string, $comment )
= $self->_rearrange( [ qw( EC_STRING COMMENT ) ], @args );
$self->init();
$EC_string && $self->EC_string( $EC_string );
$comment && $self->comment( $comment );
return $self;
} # new
=head2 init
Title : init()
Usage : $EC1->init(); # EC1 is now "-.-.-.-"
Function: Initializes this ECnumber to default values.
Returns :
Args :
=cut
sub init {
my( $self ) = @_;
$self->enzyme_class( DEFAULT );
$self->sub_class( DEFAULT );
$self->sub_sub_class( DEFAULT );
$self->serial_number( DEFAULT );
$self->comment( "" );
} # init
=head2 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 :
=cut
sub copy {
my( $self ) = @_;
my $new_ec = $self->new();
$new_ec->enzyme_class( $self->enzyme_class() );
$new_ec->sub_class( $self->sub_class() );
$new_ec->sub_sub_class( $self->sub_sub_class() );
$new_ec->serial_number( $self->serial_number() );
$new_ec->comment( $self->comment() );
return $new_ec;
} # copy
=head2 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.
=cut
sub EC_string {
my ( $self, $value ) = @_;
if ( defined $value) {
$value =~ s/\s+//g; # Removes white space.
$value =~ s/^EC//i; # Removes "EC".
$value =~ s/^://; # Removes ":".
if ( $value =~ /^([\d-]*)\.([\d-]*)\.([\d-]*)\.([\d-]*)$/ ) {
$self->enzyme_class( $1 );
$self->sub_class( $2 );
$self->sub_sub_class( $3 );
$self->serial_number( $4 );
}
else {
$self->throw( "Illegal format error [$value]" );
}
}
return $self->to_string();
} # EC_string
=head2 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 :
=cut
sub to_string {
my ( $self ) = @_;
my $s = $self->enzyme_class() . ".";
$s .= $self->sub_class() . ".";
$s .= $self->sub_sub_class() . ".";
$s .= $self->serial_number();
return $s;
} # to_string
=head2 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.
=cut
sub is_equal {
my ( $self, $value ) = @_;
if ( $self->_is_not_reference( $value ) ) {
$value = $self->new( -ec_string => $value );
}
else {
$self->_is_ECnumber_object( $value );
}
unless ( $self->enzyme_class() eq $value->enzyme_class() ) {
return FALSE;
}
unless ( $self->sub_class() eq $value->sub_class() ) {
return FALSE;
}
unless ( $self->sub_sub_class() eq $value->sub_sub_class() ) {
return FALSE;
}
unless ( $self->serial_number() eq $value->serial_number() ) {
return FALSE;
}
return TRUE;
} # is_equal
=head2 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.
=cut
sub is_member {
my ( $self, $value ) = @_;
if ( $self->_is_not_reference( $value ) ) {
$value = $self->new( -ec_string => $value );
}
else {
$self->_is_ECnumber_object( $value );
}
$self->_check_for_illegal_defaults();
$value->_check_for_illegal_defaults();
unless ( $value->enzyme_class() eq DEFAULT
|| $self->enzyme_class() eq $value->enzyme_class() ) {
return FALSE;
}
unless ( $value->sub_class() eq DEFAULT
|| $self->sub_class() eq $value->sub_class() ) {
return FALSE;
}
unless ( $value->sub_sub_class() eq DEFAULT
|| $self->sub_sub_class() eq $value->sub_sub_class() ) {
return FALSE;
}
unless ( $value->serial_number() eq DEFAULT
|| $self->serial_number() eq $value->serial_number() ) {
return FALSE;
}
return TRUE;
} # is_member
=head2 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 "-".
=cut
sub enzyme_class {
my ( $self, $value ) = @_;
if ( defined $value) {
$self->{ "_enzyme_class" } = $self->_check_number( $value );
}
return $self->{ "_enzyme_class" };
} # enzyme_class
=head2 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 "-".
=cut
sub sub_class {
my ( $self, $value ) = @_;
if ( defined $value) {
$self->{ "_sub_class" } = $self->_check_number( $value );
}
return $self->{ "_sub_class" };
} # sub_class
=head2 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 "-".
=cut
sub sub_sub_class {
my ( $self, $value ) = @_;
if ( defined $value) {
$self->{ "_sub_sub_class" } = $self->_check_number( $value );
}
return $self->{ "_sub_sub_class" };
} # sub_sub_class
=head2 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 "-".
=cut
sub serial_number {
my ( $self, $value ) = @_;
if ( defined $value) {
$self->{ "_serial_number" } = $self->_check_number( $value );
}
return $self->{ "_serial_number" };
} # serial_number
=head2 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].
=cut
sub comment {
my ( $self, $value ) = @_;
if ( defined $value) {
$self->{ "_comment" } = $value;
}
return $self->{ "_comment" };
} # comment
# Title : _check_number
# Function: Checks and standardizes the individual numbers of a EC number
# (removes leading zeros, removes white spaces).
# Returns : A standardized number.
# Args : A string representing a number in a EC number.
sub _check_number {
my ( $self, $value ) = @_;
my $original_value = $value;
$value =~ s/\s+//g; # Removes white space.
if ( $value eq "" ) {
$value = DEFAULT;
}
$value =~ s/^0+//; # Removes leading zeros.
if ( $value eq "" ) { # If it was "0" (or "00"), it would be "" now.
$value = "0";
}
elsif ( $value ne DEFAULT
&& $value =~ /\D/ ) {
$self->throw( "Illegal format error [$original_value]" );
}
return $value;
} # _check_number
# Title : _check_for_illegal_defaults()
# Function: Checks for situations like "1.-.1.1", which
# are illegal in membership tests.
# Returns :
# Args :
sub _check_for_illegal_defaults {
my ( $self ) = @_;
if ( ( $self->sub_sub_class() eq DEFAULT
&& $self->serial_number() ne DEFAULT ) ||
( $self->sub_class() eq DEFAULT
&& $self->sub_sub_class() ne DEFAULT ) ||
( $self->enzyme_class() eq DEFAULT
&& $self->sub_class() ne DEFAULT ) ) {
$self->throw( "Illegal format error for comparison ["
. $self->to_string() . "]" );
}
} # _check_for_illegal_defaults
# Title : _is_not_reference
# Function: Checks whether the argument is not a reference.
# Returns : True or false.
# Args : A scalar.
sub _is_not_reference {
my ( $self, $value ) = @_;
return ( ! ref( $value ) );
} # _is_not_reference
# Title : _is_ECnumber_object
# Function: Checks whether the arument is a ECnumber.
# Returns :
# Args : A reference.
sub _is_ECnumber_object {
my ( $self, $value ) = @_;
unless( $value->isa( "Bio::Tools::ECnumber" ) ) {
$self->throw( "Found [". ref( $value )
."] where [Bio::Tools::ECnumber] expected" );
}
} # _is_ECnumber_object
1;