Bio::Tools ECnumber
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::Tools::ECnumber - representation of EC numbers (Enzyme Classification)
Package variables
No package variables defined.
Inherit
Bio::Root::Root
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.
Methods
newDescriptionCode
initDescriptionCode
copyDescriptionCode
EC_stringDescriptionCode
to_stringDescriptionCode
is_equalDescriptionCode
is_memberDescriptionCode
enzyme_classDescriptionCode
sub_classDescriptionCode
sub_sub_classDescriptionCode
serial_numberDescriptionCode
commentDescriptionCode
_check_number
No description
Code
_check_for_illegal_defaults
No description
Code
_is_not_reference
No description
Code
_is_ECnumber_object
No description
Code
Methods description
newcode    nextTop
 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.-.-.-".
initcodeprevnextTop
 Title   : init()
Usage : $EC1->init(); # EC1 is now "-.-.-.-"
Function: Initializes this ECnumber to default values.
Returns :
Args :
copycodeprevnextTop
 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_stringcodeprevnextTop
 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_stringcodeprevnextTop
 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_equalcodeprevnextTop
 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_membercodeprevnextTop
 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_classcodeprevnextTop
 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_classcodeprevnextTop
 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 codeprevnextTop
 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_numbercodeprevnextTop
 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 "-".
commentcodeprevnextTop
 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
newdescriptionprevnextTop
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
}
initdescriptionprevnextTop
sub init {
    my( $self ) = @_;

    $self->enzyme_class( DEFAULT );
    $self->sub_class( DEFAULT );
    $self->sub_sub_class( DEFAULT );
    $self->serial_number( DEFAULT );
    $self->comment( "" );
  
} # init
}
copydescriptionprevnextTop
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
}
EC_stringdescriptionprevnextTop
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
}
to_stringdescriptionprevnextTop
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
}
is_equaldescriptionprevnextTop
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
}
is_memberdescriptionprevnextTop
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 
}
enzyme_classdescriptionprevnextTop
sub enzyme_class {
    my ( $self, $value ) = @_;

    if ( defined $value) {
        $self->{ "_enzyme_class" } = $self->_check_number( $value );
    }
   
    return $self->{ "_enzyme_class" };
    
} # enzyme_class
}
sub_classdescriptionprevnextTop
sub sub_class {
    my ( $self, $value ) = @_;

    if ( defined $value) {
        $self->{ "_sub_class" } = $self->_check_number( $value );
    }
   
    return $self->{ "_sub_class" };
    
} # sub_class
}
sub_sub_classdescriptionprevnextTop
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
}
serial_numberdescriptionprevnextTop
sub serial_number {
    my ( $self, $value ) = @_;

    if ( defined $value) {
        $self->{ "_serial_number" } = $self->_check_number( $value );
    }
   
    return $self->{ "_serial_number" };
    
} # serial_number
}
commentdescriptionprevnextTop
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.
}
_check_numberdescriptionprevnextTop
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 :
}
_check_for_illegal_defaultsdescriptionprevnextTop
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.
}
_is_not_referencedescriptionprevnextTop
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.
}
_is_ECnumber_objectdescriptionprevnextTop
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;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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/
AUTHORTop
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
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _