/ 
bioperl-1.2.2
/ Bio::Phenotype::Phenotype

NAME

Phenotype - A class for modeling phenotypes

SYNOPSIS

#get Bio::Phenotype::PhenotypeI somehow

print $phenotype->name(), "\n";
print $phenotype->description(), "\n";

my @keywords = ( "achondroplasia", "dwarfism" );
$phenotype->add_keywords( @keywords ); 
foreach my $keyword ( $phenotype->each_keyword() ) {
     print $keyword, "\n";
}
$phenotype->remove_keywords();


foreach my $gene_symbol ( $phenotype->each_gene_symbol() ) {
     print $gene_symbol, "\n";
}

foreach my $corr ( $phenotype->each_Correlate() ) {
     # Do something with $corr
}

foreach my $var ( $phenotype->each_Variant() ) {
     # Do something with $var (mutation)
}

foreach my $measure ( $phenotype->each_Measure() ) {
     # Do something with $measure
}

DESCRIPTION

This superclass implements common methods for classes modelling phenotypes. Bio::Phenotype::OMIM::OMIMentry is an example of an instantiable phenotype class (the design of this interface was partially guided by the need to model OMIM entries). Please note. This class provides methods to associate mutations (methods "each_Variant", ...) and genotypes (methods "each_Genotype", ...) with phenotypes. Yet, these aspects might need some future enhancements, especially since there is no "genotype" class yet.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to 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

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/

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

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

Title   : new
Usage   : $obj = Bio::Phenotype::Phenotype->new( -name         => "XY",
                                                 -description  => "This is ..." );
Function: Creates a new Phenotype object.
Returns : A new Phenotype object.
Args    : -name                           => the name
          -description                    => the description of this phenotype
          -species                        => ref to the the species
          -comment                        => a comment

init

Title   : init()
Usage   : $obj->init();   
Function: Initializes this OMIMentry to all "" and empty lists.
Returns : 
Args    :

name

Title   : name
Usage   : $obj->name( "r1" );
          or
          print $obj->name();
Function: Set/get for the name or id of this phenotype.
Returns : A name or id [scalar].
Args    : A name or id [scalar] (optional).

description

Title   : description
Usage   : $obj->description( "This is ..." );
          or
          print $obj->description();
Function: Set/get for the description of this phenotype.
Returns : A description [scalar].
Args    : A description [scalar] (optional).

species

Title   : species
Usage   : $obj->species( $species );
          or
          $species = $obj->species();
Function: Set/get for the species of this phenotype.
Returns : A species [Bio::Species].
Args    : A species [Bio::Species] (optional).

comment

Title   : comment
Usage   : $obj->comment( "putative" );
          or
          print $obj->comment();
Function: Set/get for a comment about this phenotype.
Returns : A comment [scalar].
Args    : A comment [scalar] (optional).

each_gene_symbol

Title   : each_gene_symbol()
Usage   : @gs = $obj->each_gene_symbol();
Function: Returns a list of gene symbols [scalars, most likely Strings]
          associated with this phenotype.
Returns : A list of scalars.
Args    :

add_gene_symbols

Title   : add_gene_symbols
Usage   : $obj->add_gene_symbols( @gs );
          or
          $obj->add_gene_symbols( $gs );
Function: Pushes one or more gene symbols [scalars, most likely Strings]
          into the list of gene symbols.
Returns : 
Args    : scalar(s).

remove_gene_symbols

Usage   : $obj->remove_gene_symbols();
Function: Deletes (and returns) the list of gene symbols [scalars,
          most likely Strings] associated with this phenotype.
Returns : A list of scalars.
Args    :

each_Variant

Title   : each_Variant()
Usage   : @vs = $obj->each_Variant();
Function: Returns a list of Bio::Variation::VariantI implementing objects
          associated with this phenotype.
          This is for representing the actual mutation(s) causing this 
          phenotype.
          {* The "variants" data member and its methods will/might need to be
          changed/improved in one way or another, CZ 09/06/02 *}
Returns : A list of Bio::Variation::VariantI implementing objects.
Args    :

add_Variants

Usage   : $obj->add_Variants( @vs );
          or
          $obj->add_Variants( $v );
Function: Pushes one or more Bio::Variation::VariantI implementing objects
          into the list of Variants.
Returns : 
Args    : Bio::Variation::VariantI implementing object(s).

remove_Variants

Title   : remove_Variants
Usage   : $obj->remove_Variants();
Function: Deletes (and returns) the list of Bio::Variation::VariantI implementing
          objects associated with this phenotype.
Returns : A list of Bio::Variation::VariantI implementing objects.
Args    :

each_Reference

Title   : each_Reference()
Usage   : @refs = $obj->each_Reference();                 
Function: Returns a list of Bio::Annotation::Reference objects
          associated with this phenotype.
Returns : A list of Bio::Annotation::Reference objects.
Args    :

add_References

Title   : add_References
Usage   : $obj->add_References( @refs );
          or
          $obj->add_References( $ref );                  
Function: Pushes one or more Bio::Annotation::Reference objects
          into the list of References.
Returns : 
Args    : Bio::Annotation::Reference object(s).

remove_References

Title   : remove_References()
Usage   : $obj->remove_References();
Function: Deletes (and returns) the list of Bio::Annotation::Reference objects
          associated with this phenotype.
Returns : A list of Bio::Annotation::Reference objects.
Args    :

each_CytoPosition

Title   : each_CytoPosition()
Usage   : @cps = $obj->each_CytoPosition();                 
Function: Returns a list of Bio::Map::CytoPosition objects
          associated with this phenotype.
Returns : A list of Bio::Map::CytoPosition objects.
Args    :

add_CytoPositions

Title   : add_CytoPositions
Usage   : $obj->add_CytoPositions( @cps );
          or
          $obj->add_CytoPositions( $cp );                  
Function: Pushes one or more Bio::Map::CytoPosition objects
          into the list of CytoPositions.
Returns : 
Args    : Bio::Map::CytoPosition object(s).

remove_CytoPositions

Title   : remove_CytoPositions
Usage   : $obj->remove_CytoPositions();
Function: Deletes (and returns) the list o fBio::Map::CytoPosition objects
          associated with this phenotype.
Returns : A list of Bio::Map::CytoPosition objects.
Args    :

each_Correlate

Title   : each_Correlate()
Usage   : @corrs = $obj->each_Correlate();                 
Function: Returns a list of Bio::Phenotype::Correlate objects
          associated with this phenotype.
          (Correlates are correlating phenotypes in different species;
          inspired by mouse correlates of human phenotypes in the OMIM
          database.)
Returns : A list of Bio::Phenotype::Correlate objects.
Args    :

add_Correlates

Title   : add_Correlates
Usage   : $obj->add_Correlates( @corrs );
          or
          $obj->add_Correlates( $corr );                  
Function: Pushes one or more Bio::Phenotype::Correlate objects
          into the list of Correlates.
Returns : 
Args    : Bio::Phenotype::Correlate object(s).

remove_Correlates

Title   : remove_Correlates
Usage   : $obj->remove_Correlates();
Function: Deletes (and returns) the list of Bio::Phenotype::Correlate objects
          associated with this phenotype.
Returns : A list of Bio::Phenotype::Correlate objects.
Args    :

each_Measure

Title   : each_Measure()
Usage   : @ms = $obj->each_Measure();                 
Function: Returns a list of Bio::Phenotype::Measure objects
          associated with this phenotype.
          (Measure is for biochemically defined phenotypes
          or any other types of measures.)
Returns : A list of Bio::Phenotype::Measure objects.
Args    :

add_Measures

Title   : add_Measures
Usage   : $obj->add_Measures( @ms );
          or
          $obj->add_Measures( $m );                  
Function: Pushes one or more Bio::Phenotype::Measure objects
          into the list of Measures.
Returns : 
Args    : Bio::Phenotype::Measure object(s).

remove_Measures

Title   : remove_Measures
Usage   : $obj->remove_Measures();
Function: Deletes (and returns) the list of Bio::Phenotype::Measure objects
          associated with this phenotype.
Returns : A list of Bio::Phenotype::Measure objects.
Args    :

each_keyword

Title   : each_keyword()
Usage   : @kws = $obj->each_keyword();                 
Function: Returns a list of key words [scalars, most likely Strings]
          associated with this phenotype.
Returns : A list of scalars.
Args    :

add_keywords

Title   : add_keywords
Usage   : $obj->add_keywords( @kws );
          or
          $obj->add_keywords( $kw );                  
Function: Pushes one or more keywords [scalars, most likely Strings]
          into the list of key words.
Returns : 
Args    : scalar(s).

remove_keywords

Title   : remove_keywords
Usage   : $obj->remove_keywords();
Function: Deletes (and returns) the list of key words [scalars,
          most likely Strings] associated with this phenotype.
Returns : A list of scalars.
Args    :
Title   : each_DBLink()
Usage   : @dbls = $obj->each_DBLink();                 
Function: Returns a list of Bio::Annotation::DBLink objects
          associated with this phenotype.
Returns : A list of Bio::Annotation::DBLink objects.
Args    :
Title   : add_DBLink
Usage   : $obj->add_DBLinks( @dbls );
          or
          $obj->add_DBLinks( $dbl );                  
Function: Pushes one or more Bio::Annotation::DBLink objects
          into the list of DBLinks.
Returns : 
Args    : Bio::Annotation::DBLink object(s).
Title   : remove_DBLinks
Usage   : $obj->remove_DBLinks();
Function: Deletes (and returns) the list of Bio::Annotation::DBLink objects
          associated with this phenotype.
Returns : A list of Bio::Annotation::DBLink objects.
Args    :

each_Genotype

Title   : each_Reference()
Usage   : @gts = $obj->each_Reference();                 
Function: Returns a list of "Genotype" objects
          associated with this phenotype.
          {* the "genotypes" data member and its methods certainly will/needs to be
          changed/improved in one way or another since there is
          no "Genotype" class yet, CZ 09/06/02 *}
Returns : A list of "Genotype" objects.
Args    :

add_Genotypes

Title   : add_Genotypes
Usage   : $obj->add_Genotypes( @gts );
          or
          $obj->add_Genotypes( $gt );                  
Function: Pushes one or more "Genotypes"
          into the list of "Genotypes".
Returns : 
Args    : "Genotypes(s)".

remove_Genotypes

Title   : remove_Genotypes
Usage   : $obj->remove_Genotypes();
Function: Deletes (and returns) the list of "Genotype" objects
          associated with this phenotype.
Returns : A list of "Genotype" objects.
Args    :

_check_ref_type

Title   : _check_ref_type
Usage   : $self->_check_ref_type( $value, "Bio::Annotation::DBLink" );
Function: Checks for the correct type.
Returns : 
Args    : The value to be checked, the expected class.