/ 
Genetics-0.03
River stage zero No dependents
/ Genetics::Object

NAME

Genetics::Object

SYNOPSIS

A synopsis is not appropriate, as one would never normally instantiate an instance of Genetics::Object.

See the synopses for the individual subclasses.

DESCRIPTION

This is the base class for all GenPerl objects.

For more information, see the GenPerl tutorial and the documentation for the individual sub-classes. Also, see Genetics::API for a description of the GenPerl database interface.

LICENSE

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

FEEDBACK

Currently, all feedback should be sent directly to the author.

AUTHOR - Steve Mathias

Email: mathias@genomica.com

Phone: (720) 565-4029

Address: Genomica Corporation 1745 38th Street Boulder, CO 80301

DETAILS

The rest of the documentation describes each of the object variables and methods. The names of internal variables and methods are preceded with an underscore (_).

Imported Packages

strict		Just to be anal
vars			Global variables
Carp			Error reporting
XML::Writer           Used by generateXML methods
HTML::Template        Used by asHTML methods

Genetics::Cluster     Subclass
Genetics::DNASample   Subclass
Genetics::FrequencySource Subclass
Genetics::Genotype    Subclass
Genetics::Haplotype   Subclass
Genetics::HtMarkerCollection Subclass
Genetics::Kindred     Subclass
Genetics::Map         Subclass
Genetics::Marker      Subclass
Genetics::Phenotype   Subclass
Genetics::SNP         Subclass
Genetics::StudyVariable Subclass
Genetics::Subject     Subclass
Genetics::TissueSample Subclass

Public methods

new

Function  : Object constructor
Arguments : Class name and hash array
Returns   : Blessed hash
Scope     : Public
Called by : Main
Comments  : Creates an empty hash, blesses it into the class name and calls
            _initialize with the arguments passed

new

Function  : Return the object type: Subject, Genotype, etc.
Arguments : A Genetics::Object object.
Returns   : Scalar
Scope     : Public
Comments  :

field

Function  : Get or set specified field data
Argument  : Field name and value (both optional)
Returns   : Called with a single argument, this returns the value of the field 
            named by the argument.  Called with tow argumetns, this sets the 
            value of the field named by the first argument to the value in the 
            second argument.  Called with no arguments, this returns a list of 
            all field names.
Scope     : Public
Called by : 
Comments  : As an alternative to using this method, field names can be used as 
            get/set methods (see AUTOLOAD).

print

Function  : Print out object in a raw format
Argument  : N/A
Returns   : N/A
Scope     : Public
Called by : Main
Comments  : This is mostly for debugging purposes.

dump

Function  : Same as print, but returns a string instead of printing it.
Argument  : N/A
Returns   : Scalar text string.
Scope     : Public
Called by : Main
Comments  : This is mostly for debugging purposes.

printObjectXML

Function  : Generate and print XML common to all Genperl objects. 
Argument  : A Genetics::Object object and the XML::Writer object being used 
            to generate the XML.
Returns   : N/A
Scope     : Public Instance Method
Called by : printXML methods of Genetics::Object subclasses.
Comments  :

toStone

Function  : 
Arguments : 
Returns   : 
Example   : toStone()
Scope     : Public instance method
Comments  :

AUTOLOAD

Function  : Allow field names to be used as get/set methods instead of field().
Argument  : Optional field value, in which case the field is set to this new 
            value (see field())
Returns   : Field value
Scope     : Public
Called by : Called automatically when an undefined method - in 
            Genetics::Object, or any of its subclasses - is invoked.

DESTROY

Function  : Deallocate object storage
Argument  : N/A
Returns   : N/A
Scope     : Public
Called by : Called automatically when the object goes out of scope 
            (ie the internal reference count in the symbol table is 
            zero).  Can be called explicitly.

Private methods

_initialize

Function  : Initialize object
Arguments : Hash array of attributes/values passed to new()
Returns   : N/A
Scope     : Private
Called by : 
Comments  :

_setDefaults

Function  : Set default attribute values
Arguments : 
Returns   : N/A
Scope     : Private
Called by : Genetics::Object->_initialize
Comments  :

_verifyRequired

Function  : Verify that required attributes are set
Arguments : N/A
Returns   : N/A
Scope     : Private
Called by : Genetics::Object->_initialize()
Comments  : Verify that required fields have values.

_generalHTMLParam

Function  : Generate parameter hash, for passing to HTML::Template, 
            containing data common to all Genperl objects. 
Argument  : A Genetics::Object object and a reference to a parameter hash.
Returns   : N/A
Scope     : Private Instance Method
Called by : asHTML methods of Genetics::Object subclasses.
Comments  :

_attr2String

Function  : Convert a pointer to a complex attribute value into a string 
            for printing.
Arguments : N/A
Returns   : N/A
Scope     : Private Class Method
Called by : print().  _instantiate() and field() also call this method when 
            the debug flag is set.
Comments  : Recurses if nested pointers exist in the data structure.