Genetics::Object
A synopsis is not appropriate, as one would never normally instantiate an instance of Genetics::Object.
See the synopses for the individual subclasses.
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.
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
Currently, all feedback should be sent directly to the author.
Email: mathias@genomica.com
Phone: (720) 565-4029
Address: Genomica Corporation 1745 38th Street Boulder, CO 80301
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 (_).
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
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
Function : Return the object type: Subject, Genotype, etc. Arguments : A Genetics::Object object. Returns : Scalar Scope : Public Comments :
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).
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.
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.
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 :
Function : Arguments : Returns : Example : toStone() Scope : Public instance method Comments :
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.
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.
Function : Initialize object Arguments : Hash array of attributes/values passed to new() Returns : N/A Scope : Private Called by : Comments :
Function : Set default attribute values Arguments : Returns : N/A Scope : Private Called by : Genetics::Object->_initialize Comments :
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.
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 :
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.
To install Genetics, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Genetics
CPAN shell
perl -MCPAN -e shell install Genetics
For more information on module installation, please visit the detailed CPAN module installation guide.