Bio::Phenotype
Measure
Summary
Measure - Representation of context/value(-range)/unit triplets
Package variables
No package variables defined.
Included modules
Inherit
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.
Methods
Methods description
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 |
Title : init()
Usage : $measure->init();
Function: Initializes this Measure to all "".
Returns :
Args : |
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). |
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). |
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). |
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). |
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). |
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). |
Title : to_string()
Usage : print $measure->to_string();
Function: To string method for Measure objects.
Returns : A string representations of this Measure.
Args : |
Methods code
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;
}
} | sub init
{ my( $self ) = @_;
$self->context( "" );
$self->description( "" );
$self->start( "" );
$self->end( "" );
$self->unit( "" );
$self->comment( "" );
}
} | sub context
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_context" } = $value;
}
return $self->{ "_context" };
}
} | sub description
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_description" } = $value;
}
return $self->{ "_description" };
}
} | sub start
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_start" } = $value;
}
return $self->{ "_start" };
}
} | sub end
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_end" } = $value;
}
return $self->{ "_end" };
}
} | sub unit
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_unit" } = $value;
}
return $self->{ "_unit" };
}
} | sub comment
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_comment" } = $value;
}
return $self->{ "_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;
}
} | General documentation
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://bio.perl.org/MailList.html - About the mailing lists
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
The rest of the documentation details each of the object
methods.