AFLPcore
Class SizeStandard

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

public class SizeStandard

extends Operation

This class is used to define a size standard. As far as this program is concerned, a size standard only contains the size in bp of the expected values. For example, something like: 50, 75, 100, 150, etc... The program can then use these to tell which values read in from a file are valid points. Size standards are read in from the file "standards.cfg" and stored in this class.

Fields inherited from class AFLPcore.Operation

descript, helpFile, name, options

Method Summary

void	add(double value) Adds the specified value to the defintion.
boolean	contains(double value) Tells whether or not the specified value is included in this size standard definition.
java.lang.String	getDescription() Defined to satisfy abstract parent class, but not really applicable in this case.
java.lang.String	getHelpFile() Defined to satisfy abstract parent class, but not really applicable in this case.
java.lang.String	getName() Gives the name of this size standard.
Option[]	getOptions() Defined to satisfy abstract parent class, but not really applicable in this case.
double	getPeakLocation(int peakIndex) Returns the location of a peak at a given index
int	getSize() Returns the number of elements conained within the datalist
void	setOptions(Option[] opts) Defined to satisfy abstract parent class, but not really applicable in this case.

Methods inherited from class java.lang.Object

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

Method Detail

getName

public java.lang.String getName()

Gives the name of this size standard.

Overrides:

getName in class Operation

Returns:

the name.

contains

public boolean contains(double value)

Tells whether or not the specified value is included in this size standard definition.

Parameters:

value - the size in bp

Returns:

true if it contains the value.

add

public void add(double value)

Adds the specified value to the defintion.

Parameters:

value - the value to add, in bp

getDescription

public java.lang.String getDescription()

Defined to satisfy abstract parent class, but not really applicable in this case.

Overrides:

getDescription in class Operation

Following copied from class: AFLPcore.Operation

Returns:

the description

getHelpFile

public java.lang.String getHelpFile()

Defined to satisfy abstract parent class, but not really applicable in this case.

Overrides:

getHelpFile in class Operation

Following copied from class: AFLPcore.Operation

Returns:

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

getOptions

public Option[] getOptions()

Defined to satisfy abstract parent class, but not really applicable in this case.

Overrides:

getOptions in class Operation

Following copied from class: AFLPcore.Operation

Returns:

the options, null if there are none.

setOptions

public void setOptions(Option[] opts)

Defined to satisfy abstract parent class, but not really applicable in this case.

Overrides:

setOptions in class Operation

Following copied from class: AFLPcore.Operation

Parameters:

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

getSize

public int getSize()

Returns the number of elements conained within the datalist

getPeakLocation

public double getPeakLocation(int peakIndex)

Returns the location of a peak at a given index