AFLPcore
Class NoSize

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

All Implemented Interfaces:

java.lang.Cloneable

public class NoSize

extends SizeFunction

This class will not provide any sizing. However, it can be useful if one wants to show how different lanes ran. It works on the assumption, which is obviously false, that size = scan#. Therefore, this sizing function provides a way to get the scan numbers easily and without using different calls at other points in a program. Since it simply assumes that they are equal, it does not need to be initialized, nor does it have any options.

See Also:

SizeFunction, LocalSouthern

Fields inherited from class AFLPcore.Operation

descript, helpFile, name, options

Constructor Summary

NoSize()
Create a new NoSize object, which will just use scan numbers as the size.

Method Summary

java.lang.String	getDescription() Gives a brief description of this sizing function.
java.lang.String	getHelpFile() Gives the help file that describes the function in more detail
java.lang.String	getName() Gives the name describing this sizing function.
Option[]	getOptions() There are no options for this sizing function.
int	getScan(double size) Gives the input value back as the scan number since the size is the scan number in this case.
double	getSize(int scan) Gives the scan number back as the size.
void	init(DataList standardPeaks) Since this class does not really perform any sizing and instead just assumes that size=scan#, there is no need to initialize it with known points.
void	read(java.io.DataInputStream in) Reads in the properties of this class from the specified input stream.
void	setMaxScan(int max) This class simply interprests the size number as the scan number, so the maximum scan number is not really needed.
void	setOptions(Option[] opts) Since there are no options, this method doesn't do much.
void	write(java.io.DataOutputStream out) Writes all of the information this class needs to store in order to be recreated.

Methods inherited from class AFLPcore.SizeFunction

clone

Methods inherited from class java.lang.Object

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

Constructor Detail

NoSize

public NoSize()

Create a new NoSize object, which will just use scan numbers as the size.

Method Detail

getName

public java.lang.String getName()

Gives the name describing this sizing function.

Overrides:

getName in class Operation

Returns:

the name

getDescription

public java.lang.String getDescription()

Gives a brief description of this sizing function.

Overrides:

getDescription in class Operation

Returns:

a one sentence explination.

getHelpFile

public java.lang.String getHelpFile()

Gives the help file that describes the function in more detail

Overrides:

getHelpFile in class Operation

Returns:

a plaintext of html help file.

getOptions

public Option[] getOptions()

There are no options for this sizing function.

Overrides:

getOptions in class Operation

Returns:

null

setOptions

public void setOptions(Option[] opts)

Since there are no options, this method doesn't do much. In fact, it does absolutely nothing, but it is required by the abstract class Operation, which this class is a child of.

Overrides:

setOptions in class Operation

Following copied from class: AFLPcore.Operation

Parameters:

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

init

public void init(DataList standardPeaks)

Since this class does not really perform any sizing and instead just assumes that size=scan#, there is no need to initialize it with known points. Therefore, this method does not do anything to this class.

Overrides:

init in class SizeFunction

Parameters:

standardPeaks - a list of peaks

getSize

public final double getSize(int scan)

Gives the scan number back as the size. This has the affect of not sizing the lane.

Overrides:

getSize in class SizeFunction

Parameters:

scan - the scan number to determine the size for.

Returns:

the scan number scan

getScan

public final int getScan(double size)

Gives the input value back as the scan number since the size is the scan number in this case.

Overrides:

getScan in class SizeFunction

Parameters:

size - the size in bp, which is also the scan number.

Returns:

the scan number, which is also size

setMaxScan

public void setMaxScan(int max)

This class simply interprests the size number as the scan number, so the maximum scan number is not really needed.

Overrides:

setMaxScan in class SizeFunction

Parameters:

max - the maximum scan number, ignored

read

public void read(java.io.DataInputStream in)
          throws java.io.IOException

Reads in the properties of this class from the specified input stream. The stream data should have been created by write. This will retrieve this classes state from the input stream. All of the current data in this class will be replaced.

Overrides:

read in class SizeFunction

Parameters:

in - the input stream with the data for the class.

Throws:

java.io.IOException - occurs when a problem is encountered when reading from the stream.

write

public void write(java.io.DataOutputStream out)
           throws java.io.IOException

Writes all of the information this class needs to store in order to be recreated. This will be used for things like storing the class in a file. Therefore, the write should output enough information so that read can recreate the essential properties of this class.

Overrides:

write in class SizeFunction

Parameters:

out - the destination to write the data to.

Throws:

java.io.IOException - occurs when a problem is encountered when writing to the stream.