NAME

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

SYNOPSIS

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

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

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 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

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.

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    :

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq