Bio::Phenotype::Measure - Representation of context/value(-range)/unit triplets

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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Bio::Phenotype::Measure - Representation of context/value(-range)/unit triplets

SYNOPSIS

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  use Bio::Phenotype::Measure;

  my $measure = Bio::Phenotype::Measure->new( -context     => "length",
                                              -description => "reduced length in 4(Tas1r3)",
                                              -start       => 0,
                                              -end         => 15,
                                              -unit        => "mm",
                                              -comment     => "see also Miller et al" );

  print $measure->context();
  print $measure->description();
  print $measure->start();
  print $measure->end();
  print $measure->unit();
  print $measure->comment();

  print $measure->to_string();

DESCRIPTION

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Measure is for biochemically defined phenotypes or any other types of measures.

FEEDBACK

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Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of 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

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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

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The rest of the documentation details each of the object methods.

new

 Title   : new
 Usage   : my $me = Bio::Phenotype::Measure->new( -context     => "length",
                                                  -description => "reduced length in 4(Tas1r3)",
                                                  -start       => 0,
                                                  -end         => 15,
                                                  -unit        => "mm",
                                                  -comment     => "see Miller also et al" );                      
 Function: Creates a new Measure object.
 Returns : A new Measure object.
 Args    : -context     => the context
           -description => a description
           -start       => the start value
           -end         => the end value
           -unit        => the unit
           -comment     => a comment

init

 Title   : init()
 Usage   : $measure->init();   
 Function: Initializes this Measure to all "".
 Returns : 
 Args    :

context

 Title   : context
 Usage   : $measure->context( "Ca-conc" );
           or 
           print $measure->context(); 
 Function: Set/get for the context of this Measure.
 Returns : The context.
 Args    : The context (optional).

description

 Title   : description
 Usage   : $measure->description( "reduced in 4(Tas1r3)" );
           or 
           print $measure->description(); 
 Function: Set/get for the description of this Measure.
 Returns : A description.
 Args    : A description (optional).

start 

 Title   : start
 Usage   : $measure->start( 330 );
           or 
           print $measure->start(); 
 Function: Set/get for the start value of this Measure.
 Returns : The start value.
 Args    : The start value (optional).

end 

 Title   : end 
 Usage   : $measure->end( 459 );
           or 
           print $measure->end(); 
 Function: Set/get for the end value of this Measure.
 Returns : The end value.
 Args    : The end value (optional).

unit

 Title   : unit
 Usage   : $measure->unit( "mM" );
           or 
           print $measure->unit(); 
 Function: Set/get for the unit of this Measure.
 Returns : The unit.
 Args    : The unit (optional).

comment

 Title   : comment
 Usage   : $measure->comment( "see also Miller et al" );
           or 
           print $measure->comment();
 Function: Set/get for an arbitrary comment about this Measure.
 Returns : A comment.
 Args    : A comment (optional).

to_string

 Title   : to_string()
 Usage   : print $measure->to_string();
 Function: To string method for Measure objects.
 Returns : A string representations of this Measure.
 Args    :
BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::Phenotype::Measure
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Christian M. Zmasek <czmasek-at-burnham.org> or <cmzmasek@yahoo.com>
#
# (c) Christian M. Zmasek, czmasek-at-burnham.org, 2002.
# (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
#
# You may distribute this module under the same terms as perl itself.
# Refer to the Perl Artistic License (see the license accompanying this
# software package, or see http://www.perl.com/language/misc/Artistic.html)
# for the terms under which you may use, modify, and redistribute this module.
#
# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code



# Let the code begin...

package Bio::Phenotype::Measure;
use strict;

use base qw(Bio::Root::Root);



sub new {
    my( $class, @args ) = @_;
    
    my $self = $class->SUPER::new( @args );

    my ( $con, $desc, $start, $end, $unit, $comment )
    = $self->_rearrange( [ qw( CONTEXT
                               DESCRIPTION
                               START
                               END
                               UNIT
                               COMMENT ) ], @args );

    $self->init(); 
 
    $con     && $self->context( $con );
    $desc    && $self->description( $desc );
    $start   && $self->start( $start );
    $end     && $self->end( $end );
    $unit    && $self->unit( $unit );
    $comment && $self->comment( $comment );
                           
    return $self;
    
} # new





sub init {
    my( $self ) = @_;

    $self->context( "" );
    $self->description( "" );
    $self->start( "" );
    $self->end( "" );
    $self->unit( "" );
    $self->comment( "" );
  
} # init





sub context {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_context" } = $value;
    }
   
    return $self->{ "_context" };
    
} # context





sub description {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_description" } = $value;
    }
   
    return $self->{ "_description" };
    
} # description





sub start {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_start" } = $value;
    }
   
    return $self->{ "_start" };
    
} #  start





sub end {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_end" } = $value;
    }
   
    return $self->{ "_end" };
    
} # end





sub unit {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_unit" } = $value;
    }
   
    return $self->{ "_unit" };
    
} # unit





sub comment {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_comment" } = $value;
    }
   
    return $self->{ "_comment" };
    
} # comment





sub to_string {
    my ( $self ) = @_;

    my $s = "";
    
    $s .= "-- Context:\n";
    $s .= $self->context()."\n";
    $s .= "-- Description:\n";
    $s .= $self->description()."\n";
    $s .= "-- Start:\n";
    $s .= $self->start()."\n";
    $s .= "-- End:\n";
    $s .= $self->end()."\n";
    $s .= "-- Unit:\n";
    $s .= $self->unit()."\n";
    $s .= "-- Comment:\n";
    $s .= $self->comment();
    
    return $s;
    
} # to_string



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