org.metaqtl
Class Qtl

java.lang.Object
  extended by org.metaqtl.Qtl

public class Qtl
extends java.lang.Object

A QTL (Quantitative Trait Loci)


Nested Class Summary
 class Qtl.QTLCross
          This class stores the informations on the cross design used to detect the QTL.
 class Qtl.QTLProj
          This class stores the QTL projection properties.
 class Qtl.QTLStats
          This class stores the usual statistics for the QTL.
 class Qtl.QTLSupport
          This class stores information on the QTL Confidence Interval
 class Qtl.QTLTrait
          This class stores the trait description of a QTL
 
Field Summary
 double c1
          The recombination rate between the QTL position and the left flanking marker.
 double c2
          The recombination rate between the QTL position and the right flanking marker.
 Qtl.QTLSupport ci
          The QTL confidence interval.
 Qtl.QTLCross cross
          The QTL cross design.
 int id
          The id of the Qtl
 int m1
          The indice of the left flanking marker.
 int m2
          The indice of the right flanking marker.
 java.lang.String name
          The name of the QTL.
 double position
          The QTL most probable location on the chromosome.
 Qtl.QTLProj proj
          The QTL projection properties.
 double sd_position
          The standard deviation of the QTL position.
 Qtl.QTLStats stats
          The QTL statistics
 Qtl.QTLTrait trait
          The QTL trait data.
 
Constructor Summary
Qtl()
           
 
Method Summary
 Qtl getCopy()
          Returns a copy of the QTL.
 java.lang.String getName()
          Returns the name of the QTL.
static double getQTLSD(double rsquare, Qtl.QTLCross cross, int mappingUnit)
          Depending on the r-square parameter and the cross design this method returns the standard deviation of the QTL position for the given mapping context.
static double getQTLSD(Qtl.QTLSupport ci, int mappingFunction, int mappingUnit)
          Depending on the CI type this methods returns the the standard deviation of the QTL position using the given mapping context.
 boolean isIgnore()
          This methods returns true if the QTL must be ignored.
 void setIgnore(boolean ignore)
          Set the status of the QTL.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

id

public int id
The id of the Qtl


name

public java.lang.String name
The name of the QTL.


m1

public int m1
The indice of the left flanking marker.


m2

public int m2
The indice of the right flanking marker.


position

public double position
The QTL most probable location on the chromosome.


sd_position

public double sd_position
The standard deviation of the QTL position.


c1

public double c1
The recombination rate between the QTL position and the left flanking marker.


c2

public double c2
The recombination rate between the QTL position and the right flanking marker.


trait

public Qtl.QTLTrait trait
The QTL trait data.


stats

public Qtl.QTLStats stats
The QTL statistics


ci

public Qtl.QTLSupport ci
The QTL confidence interval.


cross

public Qtl.QTLCross cross
The QTL cross design.


proj

public Qtl.QTLProj proj
The QTL projection properties.

Constructor Detail

Qtl

public Qtl()
Method Detail

getQTLSD

public static double getQTLSD(Qtl.QTLSupport ci,
                              int mappingFunction,
                              int mappingUnit)
Depending on the CI type this methods returns the the standard deviation of the QTL position using the given mapping context.

Parameters:
ci - the confidence interval of the QTL.
mappingFunction - the mapping function.
mappingUnit - the mapping unit.
Returns:
the standard deviation of the QTL position.

getQTLSD

public static double getQTLSD(double rsquare,
                              Qtl.QTLCross cross,
                              int mappingUnit)
Depending on the r-square parameter and the cross design this method returns the standard deviation of the QTL position for the given mapping context. This method uses the formula introduced in Darvasi A. and Soller M., A Simple Method to Calculate Resolving Power and Confidence Interval of QTL Map Location, 1997, Behavior Genetics 27,2:125-132. For the moment the cross type is not taken into account.

Parameters:
rsquare -
Returns:

isIgnore

public boolean isIgnore()
This methods returns true if the QTL must be ignored.

Returns:
true if the QTL must be ignored.

setIgnore

public void setIgnore(boolean ignore)
Set the status of the QTL.

Parameters:
ignore - the status of the QTL.

getCopy

public Qtl getCopy()
Returns a copy of the QTL.

Returns:
a copy of the QTL.

getName

public java.lang.String getName()
Returns the name of the QTL.

Returns:
the name of the QTL.