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Introduction

 

In this section we explain the meaning of a class and overview Visual Gene Developer's classes.

 


o What is a class?

"In object-oriented programming, a class is a construct that is used as a blueprint (or template) to create objects of that class. This blueprint describes the state and behavior that the objects of the class all share. An object of a given class is called an instance of the class. The class that contains (and was used to create) that instance can be considered as the type of that object. A class usually represents a noun, such as a person, place or (possibly quite abstract) thing - it is a model of a concept within a computer program. Fundamentally, it encapsulates the state and behavior of the concept it represents. It encapsulates state through data placeholders called attributes (or member variables or instance variables); it encapsulates behavior through reusable sections of code called methods. More technically, a class is a cohesive package that consists of a particular kind of metadata. A class has both an interface and a structure. The interface describes how to interact with the class and its instances with methods, while the structure describes how the data is partitioned into attributes within an instance. A class may also have a representation (metaobject) at run time, which provides run time support for manipulating the class-related metadata. In object-oriented design, a class is the most specific type of an object in relation to a specific layer"

From Wikipedia, click here for more details (http://en.wikipedia.org/wiki/Class_(computer_science))

 

Since it is hard to understand the concept of a class, we simply define a class as

A reproducible object that contains modules such as function routine, sub routine, and property (=attribute).

 

Function routine: It returns a value. It is used mainly to calculate something.

Sub routine: It doesn't return a value. It is used mainly to perform a certain work.

Property: It works as a variable. A user can read (or write) value via a property.

 

 


o Summary of Visual Gene Developer's class

 

 Class

Description

Example

 AppService

 General application service

 - Exporting data to clipboard

 - Showing message

 GeneService

 Gene analysis related modules

 - Calculating CAI or GC content

 - Getting codon usage table

 GeneConstruct

 Allows to access gene construct memory array and gene analysis table

 - Reading sequence data

 - Generating new gene construct

 LayerView

 Allows to access 'Layer view manager' and includes graphic modules

 - Drawing local GC content diagram along DNA sequence

 mRNApredict

 mRNA secondary structure prediction

 - Predicting mRNA structure

 - Calculating Gibbs free energy

 CustomUI

 Custom UI (User interface) form and graphics engine

 - Draw line, circle, pie, string

 - Export image and raw data

 NeuralNet

 Artificial neural network prediction modules

 - Loading trained neural network file

 - Predicting new data set

 NetComService

 Network and multi-threaded computing modules

 - Controlling network connection

 - Developing new module for network computing

 PropertyBag

 Allows to access PropertyBag to read and write parameter values

 - Reading parameter values

 - Modifying PropertyBag

 ScriptService

 A user can access other script modules

 - Calling developed modules

 - Scanning registered modules