Raw content of Bio::Phenotype::Correlate # $Id: Correlate.pm,v 1.5 2002/12/12 18:27:01 czmasek Exp $ # # BioPerl module for Bio::Phenotype::Correlate # # 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. # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Correlate - Representation of a correlating phenotype in a given species =head1 SYNOPSIS use Bio::Phenotype::Correlate; $co = Bio::Phenotype::Correlate->new( -name => "4(Tas1r3)", -description => "mouse correlate of human phenotype MIM 605865", -species => $mouse, -type => "homolog", -comment => "type=homolog is putative" ); print $co->name(); print $co->description(); print $co->species()->binomial(); print $co->type(); print $co->comment(); print $co->to_string(); =head1 DESCRIPTION This class models correlating phenotypes. Its creation was inspired by the OMIM database where many human phenotypes have a correlating mouse phenotype. Therefore, this class is intended to be used together with a phenotype class. =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. =cut # Let the code begin... package Bio::Phenotype::Correlate; use vars qw( @ISA ); use strict; use Bio::Root::Object; use Bio::Species; @ISA = qw( Bio::Root::Root ); =head2 new Title : new Usage : $co = Bio::Phenotype::Correlate->new( -name => "4(Tas1r3)", -description => "mouse correlate of human phenotype MIM 605865", -species => $mouse, -type => "homolog", -comment => "type=homolog is putative" ); Function: Creates a new Correlate object. Returns : A new Correlate object. Args : -name => a name or id -description => a description -species => the species of this correlating phenotype [Bio::Species] -type => the type of correlation -comment => a comment =cut sub new { my( $class, @args ) = @_; my $self = $class->SUPER::new( @args ); my ( $name, $desc, $species, $type, $comment ) = $self->_rearrange( [ qw( NAME DESCRIPTION SPECIES TYPE COMMENT ) ], @args ); $self->init(); $name && $self->name( $name ); $desc && $self->description( $desc ); $species && $self->species( $species ); $type && $self->type( $type ); $comment && $self->comment( $comment ); return $self; } # new =head2 init Title : init() Usage : $co->init(); Function: Initializes this Correlate to all "". Returns : Args : =cut sub init { my( $self ) = @_; $self->name( "" ); $self->description( "" ); my $species = Bio::Species->new(); $species->classification( qw( species Undetermined ) ); $self->species( $species ); $self->type( "" ); $self->comment( "" ); } # init =head2 name Title : name Usage : $co->name( "4(Tas1r3)" ); or print $co->name(); Function: Set/get for the name or id of this Correlate. Returns : The name or id of this Correlate. Args : The name or id of this Correlate (optional). =cut sub name { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_name" } = $value; } return $self->{ "_name" }; } # name =head2 description Title : description Usage : $co->description( "mouse correlate of human phenotype MIM 03923" ); or print $co->description(); Function: Set/get for the description of this Correlate. Returns : A description of this Correlate. Args : A description of this Correlate (optional). =cut sub description { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_description" } = $value; } return $self->{ "_description" }; } # description =head2 species Title : species Usage : $co->species( $species ); or $species = $co->species(); Function: Set/get for the species of this Correlate. Returns : The Bio::Species of this Correlate [Bio::Species]. Args : The Bio::Species of this Correlate [Bio::Species] (optional). =cut sub species { my ( $self, $value ) = @_; if ( defined $value ) { $self->_check_ref_type( $value, "Bio::Species" ); $self->{ "_species" } = $value; } return $self->{ "_species" }; } # species =head2 type Title : type Usage : $co->type( "homolog" ); or print $co->type(); Function: Set/get for the type of this Correlate. Returns : The type of this Correlate. Args : The type of this Correlate (optional). =cut sub type { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_type" } = $value; } return $self->{ "_type" }; } # type =head2 comment Title : comment Usage : $co->comment( "doubtful" ); or print $co->comment(); Function: Set/get for an arbitrary comment about this Correlate. Returns : A comment. Args : A comment (optional). =cut sub comment { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_comment" } = $value; } return $self->{ "_comment" }; } # comment =head2 to_string Title : to_string() Usage : print $co->to_string(); Function: To string method for Correlate objects. Returns : A string representations of this Correlate. Args : =cut sub to_string { my ( $self ) = @_; my $s = ""; $s .= "-- Name:\n"; $s .= $self->name()."\n"; $s .= "-- Description:\n"; $s .= $self->description()."\n"; $s .= "-- Species:\n"; $s .= $self->species()->binomial()."\n"; $s .= "-- Type of correlation:\n"; $s .= $self->type()."\n"; $s .= "-- Comment:\n"; $s .= $self->comment(); return $s; } # to_string # Title : _check_ref_type # Function: Checks for the correct type. # Returns : # Args : The value to be checked, the expected class. sub _check_ref_type { my ( $self, $value, $expected_class ) = @_; if ( ! defined( $value ) ) { $self->throw( ( caller( 1 ) )[ 3 ] .": Found [undef" ."] where [$expected_class] expected" ); } elsif ( ! ref( $value ) ) { $self->throw( ( caller( 1 ) )[ 3 ] .": Found scalar" ." where [$expected_class] expected" ); } elsif ( ! $value->isa( $expected_class ) ) { $self->throw( ( caller( 1 ) )[ 3 ] .": Found [". ref( $value ) ."] where [$expected_class] expected" ); } } # _check_ref_type 1;