Bio::Phenotype::Correlate - Representation of a correlating phenotype in a given species

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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Bio::Phenotype::Correlate - Representation of a correlating phenotype in a given species

SYNOPSIS

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  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();

DESCRIPTION

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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.

FEEDBACK

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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

Support

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 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/

AUTHOR

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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

APPENDIX

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The rest of the documentation details each of the object methods.

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

init

 Title   : init()
 Usage   : $co->init();   
 Function: Initializes this Correlate to all "".
 Returns : 
 Args    :

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).

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).

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).

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).

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).

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    :
BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::Phenotype::Correlate
#
# 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.
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code



# Let the code begin...

package Bio::Phenotype::Correlate;
use strict;
use Bio::Species;

use base qw(Bio::Root::Root);



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





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





sub name {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_name" } = $value;
    }

    return $self->{ "_name" };

} # name





sub description {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_description" } = $value;
    }

    return $self->{ "_description" };

} # description





sub species {

    my ( $self, $value )  = @_;

    if ( defined $value ) {
        $self->_check_ref_type( $value, "Bio::Species" );
        $self->{ "_species" } = $value;
    }
    
    return $self->{ "_species" };
    
} # species





sub type {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_type" } = $value;
    }

    return $self->{ "_type" };

} # type





sub comment {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_comment" } = $value;
    }
   
    return $self->{ "_comment" };
    
} # comment




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



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