#
# 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
=head1 NAME
Bio::Phenotype::Measure - Representation of context/value(-range)/unit triplets
=head1 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();
=head1 DESCRIPTION
Measure is for biochemically defined phenotypes or any other types of measures.
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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
=head1 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
=head1 APPENDIX
The rest of the documentation details each of the object
methods.
=cut
# Let the code begin...
package Bio::Phenotype::Measure;
use strict;
use base qw(Bio::Root::Root);
=head2 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
=cut
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
=head2 init
Title : init()
Usage : $measure->init();
Function: Initializes this Measure to all "".
Returns :
Args :
=cut
sub init {
my( $self ) = @_;
$self->context( "" );
$self->description( "" );
$self->start( "" );
$self->end( "" );
$self->unit( "" );
$self->comment( "" );
} # init
=head2 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).
=cut
sub context {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_context" } = $value;
}
return $self->{ "_context" };
} # context
=head2 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).
=cut
sub description {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_description" } = $value;
}
return $self->{ "_description" };
} # description
=head2 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).
=cut
sub start {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_start" } = $value;
}
return $self->{ "_start" };
} # start
=head2 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).
=cut
sub end {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_end" } = $value;
}
return $self->{ "_end" };
} # end
=head2 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).
=cut
sub unit {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_unit" } = $value;
}
return $self->{ "_unit" };
} # unit
=head2 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).
=cut
sub comment {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_comment" } = $value;
}
return $self->{ "_comment" };
} # comment
=head2 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 :
=cut
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
1;