Bio::Phenotype::Phenotype.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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    :
 
 
  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_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).
 
 
  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.