Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

       Bio::Phenotype::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://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

       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

       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    :

   each_DBLink
        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    :

   add_DBLinks
        Title   : add_DBLinks
        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).

   remove_DBLinks
        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.