Bio::Phenotype PhenotypeI
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Summary
PhenotypeI - An interface for classes modeling phenotypes
Package variables
No package variables defined.
Included modules
Bio::Annotation::DBLink
Bio::Annotation::Reference
Bio::Map::CytoPosition
Bio::Phenotype::Correlate
Bio::Phenotype::Measure
Bio::Range
Bio::Root::Root
Bio::Species
Bio::Variation::VariantI
Inherit
Bio::Root::Root
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 defines 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 interface 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.
Methods
add_CorrelatesDescriptionCode
add_CytoPositionsDescriptionCode
add_DBLinks
No description
Code
add_GenotypesDescriptionCode
add_MeasuresDescriptionCode
add_ReferencesDescriptionCode
add_VariantsDescriptionCode
add_gene_symbolsDescriptionCode
add_keywordsDescriptionCode
commentDescriptionCode
descriptionDescriptionCode
each_CorrelateDescriptionCode
each_CytoPositionDescriptionCode
each_DBLinkDescriptionCode
each_GenotypeDescriptionCode
each_MeasureDescriptionCode
each_ReferenceDescriptionCode
each_VariantDescriptionCode
each_gene_symbolDescriptionCode
each_keywordDescriptionCode
nameDescriptionCode
remove_CorrelatesDescriptionCode
remove_CytoPositionsDescriptionCode
remove_DBLinksDescriptionCode
remove_GenotypesDescriptionCode
remove_MeasuresDescriptionCode
remove_ReferencesDescriptionCode
remove_VariantsDescriptionCode
remove_gene_symbolsDescriptionCode
remove_keywordsDescriptionCode
speciesDescriptionCode
Methods description
add_Correlatescode    nextTop
 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).
add_CytoPositionscodeprevnextTop
 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).
add_GenotypescodeprevnextTop
 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)".
add_MeasurescodeprevnextTop
 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).
add_References codeprevnextTop
 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).
add_VariantscodeprevnextTop
 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).
add_gene_symbolscodeprevnextTop
 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).
add_keywordscodeprevnextTop
 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).
commentcodeprevnextTop
 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).
descriptioncodeprevnextTop
 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).
each_CorrelatecodeprevnextTop
 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 :
each_CytoPositioncodeprevnextTop
 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 :
each_DBLinkcodeprevnextTop
 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 :
each_GenotypecodeprevnextTop
 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 :
each_MeasurecodeprevnextTop
 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 :
each_ReferencecodeprevnextTop
 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 :
each_VariantcodeprevnextTop
 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 :
each_gene_symbolcodeprevnextTop
 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 :
each_keywordcodeprevnextTop
 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 :
namecodeprevnextTop
 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).
remove_CorrelatescodeprevnextTop
 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 :
remove_CytoPositionscodeprevnextTop
 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 :
remove_DBLinkscodeprevnextTop
 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 :
remove_GenotypescodeprevnextTop
 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 :
remove_MeasurescodeprevnextTop
 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 :
remove_ReferencescodeprevnextTop
 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 :
remove_VariantscodeprevnextTop
 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 :
remove_gene_symbolscodeprevnextTop
 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 :
remove_keywordscodeprevnextTop
 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 :
speciescodeprevnextTop
 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).
Methods code
add_CorrelatesdescriptionprevnextTop
sub add_Correlates {
    my ( $self ) = @_;

    $self->throw_not_implemented();
    
} # add_Correlates
}
add_CytoPositionsdescriptionprevnextTop
sub add_CytoPositions {
    my ( $self ) = @_;

    $self->throw_not_implemented();
    
} # add_CytoPositions
}
add_DBLinksdescriptionprevnextTop
sub add_DBLinks {
    my ( $self ) = @_;

    $self->throw_not_implemented();
    
} # add_DBLinks
}
add_GenotypesdescriptionprevnextTop
sub add_Genotypes {
    my ( $self ) = @_;

    $self->throw_not_implemented();
    
} # add_Genotypes
}
add_MeasuresdescriptionprevnextTop
sub add_Measures {
    my ( $self ) = @_;

    $self->throw_not_implemented();
    
} # add_Measures
}
add_ReferencesdescriptionprevnextTop
sub add_References {
    my ( $self ) = @_;

    $self->throw_not_implemented();
    
} # add_References
}
add_VariantsdescriptionprevnextTop
sub add_Variants {
    my ( $self ) = @_;

    $self->throw_not_implemented();
    
} # add_Variants
}
add_gene_symbolsdescriptionprevnextTop
sub add_gene_symbols {
    my ( $self ) = @_;

    $self->throw_not_implemented();
    
} # add_gene_symbols
}
add_keywordsdescriptionprevnextTop
sub add_keywords {
    my ( $self ) = @_;

    $self->throw_not_implemented();
    
} # add_keywords
}
commentdescriptionprevnextTop
sub comment {
    my ( $self ) = @_;

    $self->throw_not_implemented();

} # comment
}
descriptiondescriptionprevnextTop
sub description {
     my ( $self ) = @_;

    $self->throw_not_implemented();

} # description
}
each_CorrelatedescriptionprevnextTop
sub each_Correlate {
    my ( $self ) = @_;

    $self->throw_not_implemented();
    
} # each_Correlate
}
each_CytoPositiondescriptionprevnextTop
sub each_CytoPosition {
    my ( $self ) = @_;

    $self->throw_not_implemented();
    
} # each_CytoPosition
}
each_DBLinkdescriptionprevnextTop
sub each_DBLink {
    my ( $self ) = @_;

    $self->throw_not_implemented();
}
each_GenotypedescriptionprevnextTop
sub each_Genotype {
    my ( $self ) = @_;

    $self->throw_not_implemented();
    
} # each_Genotype
}
each_MeasuredescriptionprevnextTop
sub each_Measure {
    my ( $self ) = @_;

    $self->throw_not_implemented();
    
} # each_Measure
}
each_ReferencedescriptionprevnextTop
sub each_Reference {
    my ( $self ) = @_;

    $self->throw_not_implemented();
    
} # each_Reference
}
each_VariantdescriptionprevnextTop
sub each_Variant {
    my ( $self ) = @_;

    $self->throw_not_implemented();

} # each_Variant
}
each_gene_symboldescriptionprevnextTop
sub each_gene_symbol {
    my ( $self ) = @_;

    $self->throw_not_implemented();

} # each_gene_symbol
}
each_keyworddescriptionprevnextTop
sub each_keyword {
    my ( $self ) = @_;

    $self->throw_not_implemented();
    
} # each_keyword
}
namedescriptionprevnextTop
sub name {
    my ( $self ) = @_;

    $self->throw_not_implemented();

} # name
}
remove_CorrelatesdescriptionprevnextTop
sub remove_Correlates {
    my ( $self ) = @_;

    $self->throw_not_implemented();
    
} # remove_Correlates
}
remove_CytoPositionsdescriptionprevnextTop
sub remove_CytoPositions {
    my ( $self ) = @_;

    $self->throw_not_implemented();
    
} # remove_CytoPositions
}
remove_DBLinksdescriptionprevnextTop
sub remove_DBLinks {
    my ( $self ) = @_;

    $self->throw_not_implemented();

} # remove_DBLinks
}
remove_GenotypesdescriptionprevnextTop
sub remove_Genotypes {
    my ( $self ) = @_;

    $self->throw_not_implemented();
    
} # remove_Genotypes
1;
}
remove_MeasuresdescriptionprevnextTop
sub remove_Measures {
    my ( $self ) = @_;

    $self->throw_not_implemented();
    
} # remove_Measures
}
remove_ReferencesdescriptionprevnextTop
sub remove_References {
    my ( $self ) = @_;

    $self->throw_not_implemented();
    
} # remove_References
}
remove_VariantsdescriptionprevnextTop
sub remove_Variants {
    my ( $self ) = @_;

    $self->throw_not_implemented();
    
} # remove_Variants
}
remove_gene_symbolsdescriptionprevnextTop
sub remove_gene_symbols {
    my ( $self ) = @_;

    $self->throw_not_implemented();

} # remove_gene_symbols
}
remove_keywordsdescriptionprevnextTop
sub remove_keywords {
    my ( $self ) = @_;

    $self->throw_not_implemented();
    
} # remove_keywords
}
speciesdescriptionprevnextTop
sub species {
    my ( $self ) = @_;

    $self->throw_not_implemented();

} # species
}
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 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 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
email or the web:
  bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
AUTHORTop
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
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
add_DBLinkTop
 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).