uk.ac.sanger.cgp.standalonecsa.beans
Class TraceGroupBean

java.lang.Object
  uk.ac.sanger.cgp.standalonecsa.beans.TraceGroupBean

public class TraceGroupBean
extends java.lang.Object

This object is used to group the variant and wildtype experiments by amplimer. It also indicates which wildtype traces have been chosen as best normals.

Author:

Original: kr2, $Author: kr2 $

Constructor Summary

TraceGroupBean()
Creates a new instance of TraceGroupBean

Method Summary

AmplimerBean	getAmplimerData() Get the AmplimerBean assosiated with this TraceGroupBean.
ExperimentBean	getBestAntisenseWildtype() Get the best antisense/reverse wildtype ExperimentBean.
ExperimentBean	getBestSenseWildtype() Get the best sense/forward wildtype ExperimentBean.
java.util.TreeSet	getVariantTraces() Get the set of variant traces.
java.util.TreeSet	getWildtypeTraces() Get the set of wildtype traces.
void	markBestNormals() Marks the ExperimentBeans held as best[Sense|Antisense]Wildtype as best normal.
void	setAmplimerData(AmplimerBean amplimerData) Set the AmplimerBean assosiated with this TraceGroupBean.
void	setBestAntisenseWildtype(ExperimentBean bestAntisenseWildtype) Set the best antisense/reverse wildtype ExperimentBean.
void	setBestSenseWildtype(ExperimentBean bestSenseWildtype) Set the best sense/forward wildtype ExperimentBean.
void	setVariantTraces(java.util.TreeSet variantTraces) Set the new set of variant traces.
void	setWildtypeTraces(java.util.TreeSet wildtypeTraces) Set the new set of wildtype traces.
java.lang.String	toString() Get a string representation for this object.

Methods inherited from class java.lang.Object

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

Constructor Detail

TraceGroupBean

public TraceGroupBean()

Creates a new instance of TraceGroupBean

Method Detail

markBestNormals

public void markBestNormals()

Marks the ExperimentBeans held as best[Sense|Antisense]Wildtype as best normal. See ExperimentBean.setBest(boolean best).

getVariantTraces

public java.util.TreeSet getVariantTraces()

Get the set of variant traces.

Returns:

a TreeSet of variant ExperimentBeans (never returns null)

setVariantTraces

public void setVariantTraces(java.util.TreeSet variantTraces)

Set the new set of variant traces.

Parameters:

variantTraces - the new set of variant ExperimentBeans

getWildtypeTraces

public java.util.TreeSet getWildtypeTraces()

Get the set of wildtype traces.

Returns:

a TreeSet of wildtype ExperimentBeans (never returns null)

setWildtypeTraces

public void setWildtypeTraces(java.util.TreeSet wildtypeTraces)

Set the new set of wildtype traces.

Parameters:

wildtypeTraces - the new set of wildtype ExperimentBeans

getBestSenseWildtype

public ExperimentBean getBestSenseWildtype()

Get the best sense/forward wildtype ExperimentBean.

Returns:

the best sense/forward wildtype

setBestSenseWildtype

public void setBestSenseWildtype(ExperimentBean bestSenseWildtype)

Set the best sense/forward wildtype ExperimentBean.

Parameters:

bestSenseWildtype - the best sense/forward wildtype ExperimentBean.

getBestAntisenseWildtype

public ExperimentBean getBestAntisenseWildtype()

Get the best antisense/reverse wildtype ExperimentBean.

Returns:

the best antisense/reverse wildtype

setBestAntisenseWildtype

public void setBestAntisenseWildtype(ExperimentBean bestAntisenseWildtype)

Set the best antisense/reverse wildtype ExperimentBean.

Parameters:

bestAntisenseWildtype - the best antisense/reverse wildtype ExperimentBean.

getAmplimerData

public AmplimerBean getAmplimerData()

Get the AmplimerBean assosiated with this TraceGroupBean.

Returns:

the AmplimerBean for this group

setAmplimerData

public void setAmplimerData(AmplimerBean amplimerData)

Set the AmplimerBean assosiated with this TraceGroupBean.

Parameters:

amplimerData - the AmplimerBean for this group

toString

public java.lang.String toString()

Get a string representation for this object.

Overrides:

toString in class java.lang.Object

Returns:

a string representation for this object