Bio::Tools
ECnumber
Toolbar
Summary
Bio::Tools::ECnumber - representation of EC numbers (Enzyme Classification)
Package variables
No package variables defined.
Inherit
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
Methods
Methods description
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.-.-.-". |
Title : init()
Usage : $EC1->init(); # EC1 is now "-.-.-.-"
Function: Initializes this ECnumber to default values.
Returns :
Args : |
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 : |
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. |
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 : |
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. |
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. |
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 "-". |
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 "-". |
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 "-". |
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 "-". |
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]. |
Methods code
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;
}
} | sub init
{ my( $self ) = @_;
$self->enzyme_class( DEFAULT );
$self->sub_class( DEFAULT );
$self->sub_sub_class( DEFAULT );
$self->serial_number( DEFAULT );
$self->comment( "" );
}
} | 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;
}
} | sub EC_string
{ my ( $self, $value ) = @_;
if ( defined $value) {
$value =~ s/\s+//g;
$value =~ s/^EC//i;
$value =~ s/^://;
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();
}
} | 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;
}
} | 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;
}
} | 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;
}
} | sub enzyme_class
{ my ( $self, $value ) = @_;
if ( defined $value) {
$self->{ "_enzyme_class" } = $self->_check_number( $value );
}
return $self->{ "_enzyme_class" };
}
} | sub sub_class
{ my ( $self, $value ) = @_;
if ( defined $value) {
$self->{ "_sub_class" } = $self->_check_number( $value );
}
return $self->{ "_sub_class" };
}
} | sub sub_sub_class
{ my ( $self, $value ) = @_;
if ( defined $value) {
$self->{ "_sub_sub_class" } = $self->_check_number( $value );
}
return $self->{ "_sub_sub_class" };
}
} | sub serial_number
{ my ( $self, $value ) = @_;
if ( defined $value) {
$self->{ "_serial_number" } = $self->_check_number( $value );
}
return $self->{ "_serial_number" };
}
} | sub comment
{ my ( $self, $value ) = @_;
if ( defined $value) {
$self->{ "_comment" } = $value;
}
return $self->{ "_comment" };
}
} | sub _check_number
{ my ( $self, $value ) = @_;
my $original_value = $value;
$value =~ s/\s+//g;
if ( $value eq "" ) {
$value = DEFAULT;
}
$value =~ s/^0+//;
if ( $value eq "" ) {
$value = "0";
}
elsif ( $value ne DEFAULT
&& $value =~ /\D/ ) {
$self->throw( "Illegal format error [$original_value]" );
}
return $value;
}
} | 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() . "]" );
}
}
} | sub _is_not_reference
{ my ( $self, $value ) = @_;
return ( ! ref( $value ) );
}
} | | _is_ECnumber_object | description | prev | next | Top |
sub _is_ECnumber_object
{ my ( $self, $value ) = @_;
unless( $value->isa( "Bio::Tools::ECnumber" ) ) {
$self->throw( "Found [". ref( $value )
."] where [Bio::Tools::ECnumber] expected" );
}
}
1;} | General documentation
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
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.
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/
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _