AFLPcore
Class PartialSigNorm

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

public class PartialSigNorm

extends GelOperation

This class normalizes a gel. The total signal in a lane is defined as the sum of all of the points in a trace. Since the trace is simply a set of discrete points that form a curve, the total signal may also be thought of as the area under the trace curve, or as the integral over the entire size range. The lanes are normalized so that the total signal's are equal to the average signal in the gel. This class extends a gel operation. The signal in each lane is handled by the Lane class. There are no options to set.

Field Summary

static double

DEFAULT_PERCENT

Fields inherited from class AFLPcore.Operation

descript, helpFile, name, options

Constructor Summary

PartialSigNorm()
Creates a new PartialSigNorm object.

Method Summary

void	doGelOp(Gel gel) This normalizes all of the lanes in the Gel based on the signal stength of each lane.
java.lang.String	getDescription() Gives a one sentence description of this gel operation.
java.lang.String	getHelpFile() Gives a file that is the help file for this gel operation
java.lang.String	getName() Gives the name of this gel operation
Option[]	getOptions() No options for this operation, so null is returned.
void	setOptions(Option[] opts) Since there are no options for this operation, this method will do absolutely nothing.

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_PERCENT

public static double DEFAULT_PERCENT

Constructor Detail

PartialSigNorm

public PartialSigNorm()

Creates a new PartialSigNorm object.

Method Detail

doGelOp

public void doGelOp(Gel gel)

This normalizes all of the lanes in the Gel based on the signal stength of each lane.

Overrides:

doGelOp in class GelOperation

Parameters:

gel - the gel to normalize.

getOptions

public Option[] getOptions()

No options for this operation, so null is returned.

Overrides:

getOptions in class Operation

Returns:

null

setOptions

public void setOptions(Option[] opts)

Since there are no options for this operation, this method will do absolutely nothing.

Overrides:

setOptions in class Operation

Following copied from class: AFLPcore.Operation

Parameters:

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

getName

public java.lang.String getName()

Gives the name of this gel operation

Overrides:

getName in class Operation

Returns:

the name

getDescription

public java.lang.String getDescription()

Gives a one sentence description of this gel operation.

Overrides:

getDescription in class Operation

Returns:

the description

getHelpFile

public java.lang.String getHelpFile()

Gives a file that is the help file for this gel operation

Overrides:

getHelpFile in class Operation

Returns:

a plaintext of html file containing help information