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Man Pages


Manual Reference Pages  -  BIO::PHENOTYPE::PHENOTYPEI (3)

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NAME

Bio::Phenotype::PhenotypeI - An interface for classes modeling phenotypes

CONTENTS

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.

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://github.com/bioperl/bioperl-live/issues



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 _

    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    :



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