AFLPcore
Class PartialSigNorm

java.lang.Object
  |
  +--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