Raw content of Bio::Tools::ECnumber # $Id: ECnumber.pm,v 1.7 2002/12/12 18:27:02 czmasek Exp $ # # BioPerl module for Bio::Tools::ECnumber # # Cared for by Christian M. Zmasek <czmasek@gnf.org> or <cmzmasek@yahoo.com> # # (c) Christian M. Zmasek, czmasek@gnf.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 ECnumber - representation of EC numbers =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 of ECnumber objects # -------------------------------- print $EC3->EC_string( "1.01.01.001" ); # Prints "1.1.1.1". # To string # --------- 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 ECnumber is a representation of EC numbers [http://www.chem.qmul.ac.uk/iubmb/enzyme/]. =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://bio.perl.org/MailList.html - About the mailing lists =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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ =head1 AUTHOR Christian M. Zmasek Email: czmasek@gnf.org or cmzmasek@yahoo.com WWW: http://www.genetics.wustl.edu/eddy/people/zmasek/ 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 vars qw( @ISA ); use strict; use Bio::Root::Object; use constant DEFAULT => "-"; use constant TRUE => 1; use constant FALSE => 0; @ISA = 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;