Bio::Phenotype::Phenotype(3pm)				User Contributed Perl Documentation			    Bio::Phenotype::Phenotype(3pm)

NAME

       Bio::Phenotype::Phenotype - A class for modeling phenotypes

SYNOPSIS

	 #get Bio::Phenotype::PhenotypeI somehow

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

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

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

	 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.

perl v5.14.2							    2012-03-02					    Bio::Phenotype::Phenotype(3pm)