Bio::Phenotype Measure
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Summary
Bio::Phenotype::Measure - Representation of context/value(-range)/unit triplets
Package variables
No package variables defined.
Inherit
Bio::Root::Root
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
newDescriptionCode
initDescriptionCode
contextDescriptionCode
descriptionDescriptionCode
startDescriptionCode
endDescriptionCode
unitDescriptionCode
commentDescriptionCode
to_stringDescriptionCode
Methods description
newcode    nextTop
 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
initcodeprevnextTop
 Title   : init()
Usage : $measure->init();
Function: Initializes this Measure to all "".
Returns :
Args :
contextcodeprevnextTop
 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).
descriptioncodeprevnextTop
 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 codeprevnextTop
 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 codeprevnextTop
 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).
unitcodeprevnextTop
 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).
commentcodeprevnextTop
 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_stringcodeprevnextTop
 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
newdescriptionprevnextTop
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
}
initdescriptionprevnextTop
sub init {
    my( $self ) = @_;

    $self->context( "" );
    $self->description( "" );
    $self->start( "" );
    $self->end( "" );
    $self->unit( "" );
    $self->comment( "" );
  
} # init
}
contextdescriptionprevnextTop
sub context {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_context" } = $value;
    }
   
    return $self->{ "_context" };
    
} # context
}
descriptiondescriptionprevnextTop
sub description {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_description" } = $value;
    }
   
    return $self->{ "_description" };
    
} # description
}
startdescriptionprevnextTop
sub start {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_start" } = $value;
    }
   
    return $self->{ "_start" };
    
} #  start
}
enddescriptionprevnextTop
sub end {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_end" } = $value;
    }
   
    return $self->{ "_end" };
    
} # end
}
unitdescriptionprevnextTop
sub unit {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_unit" } = $value;
    }
   
    return $self->{ "_unit" };
    
} # unit
}
commentdescriptionprevnextTop
sub comment {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_comment" } = $value;
    }
   
    return $self->{ "_comment" };
    
} # comment
}
to_stringdescriptionprevnextTop
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;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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/
AUTHORTop
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
APPENDIXTop
The rest of the documentation details each of the object
methods.