AFLPcore
Class Operation

java.lang.Object
  |
  +--AFLPcore.Operation

Direct Known Subclasses:

AnalysisOp, BinOperation, CutoffFunction, GelOperation, ImportFilter, LaneOperation, PeakLocate, ScoreFunction, SizeFunction, SizeStandard

public abstract class Operation

extends java.lang.Object

This is an abstract class that should be extended to add functionality to the program. The Manager subclasses expect objects of this type. The Manager provides an easy way to access the different operations, so most of the program does not have to know what operations are available, it can find this out by quering a manager. The operation itself contains information like a name and description. It also contains a list of options that the operation can accept. However, this class should be extended so the program can know more about the operation. For example, ImportFilter extends this to read in different files.

See Also:

Manager, Option

Field Summary

protected java.lang.String	descript
protected java.lang.String	helpFile
protected java.lang.String	name
protected Option[]	options

Constructor Summary

Operation()

Method Summary

abstract java.lang.String	getDescription() Retrieves a short, approximately one sentence, description of the operation.
abstract java.lang.String	getHelpFile() Each operation should have a help file that describes its actions, types of files it works on, and an explination of any options that the filter supports.
abstract java.lang.String	getName() Access the name of the operation.
abstract Option[]	getOptions() Retrieves the options associated with this operation.
abstract void	setOptions(Option[] opts) This is used to set the options to the specified values.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

name

protected java.lang.String name

descript

protected java.lang.String descript

helpFile

protected java.lang.String helpFile

options

protected Option[] options

Constructor Detail

Operation

public Operation()

Method Detail

getName

public abstract java.lang.String getName()

Access the name of the operation. It should be somewhat unique, short, and descriptive. It's recommened to store the name internally in the name variable.

Returns:

name of the operation

getDescription

public abstract java.lang.String getDescription()

Retrieves a short, approximately one sentence, description of the operation.

Returns:

the description

getHelpFile

public abstract java.lang.String getHelpFile()

Each operation should have a help file that describes its actions, types of files it works on, and an explination of any options that the filter supports.

Returns:

Filename that contains the help information, either html or plaintext.

getOptions

public abstract Option[] getOptions()

Retrieves the options associated with this operation. In some cases, these may be required parameters, but this method provides a way for other classes to query this object and determine it's requirements.

Returns:

the options, null if there are none.

setOptions

public abstract void setOptions(Option[] opts)

This is used to set the options to the specified values. These may be required before a operation can be performed.

Parameters:

opts - the values for the options that this operation understands.