object.microarray
Class ElementMap

java.lang.Object
  object.microarray.ElementMap

All Implemented Interfaces:

java.io.Serializable

public class ElementMap
extends java.lang.Object
implements java.io.Serializable

Description
ElementMap Object
Infos : KLB - IPMC - 07/2004

See Also:

Serialized Form

Field Summary

private java.lang.String	bloc Bloc in which the oligo is located
private java.lang.String	column Column in Bloc in which the oligo is located
private java.lang.String	cy3_bruit Cy3 Signal Background of the spot
private java.lang.String	cy3_median Cy3 Signal of the spot
private java.lang.String	cy5_bruit Cy5 Signal Background of the spot
private java.lang.String	cy5_median Cy5 Signal of the spot
private boolean	flag Flag true or false of the spot
private java.lang.String	flag_str Flag string of the spot
private boolean	is_adhoc if this oligo is an adhoc oligo
private boolean	is_control if this oligo is an oligo control
private boolean	is_externe if this oligo is an external oligo
private boolean	is_tiling if this oligo is a tiling oligo
private int	oligo_id ID of Oligo object of this ElementMap
private java.lang.String	oligo_id_str ID String of Oligo object of this ElementMap
private java.lang.String	ratio Ratio Signal of the spot
private int	rayon rayon of the oligo on the Tiff image
private java.lang.String	row Row in Bloc in which the oligo is located
private java.lang.String	symbol Symbol of Oligo object of this ElementMap
private int	x_coord X_coord of the oligo on the Tiff image
private int	y_coord Y_coord of the oligo on the Tiff image

Constructor Summary

ElementMap()
Default constructor

ElementMap(java.lang.String symbol, java.lang.String oid, int x_coord, int y_coord, int rayon, java.lang.String cy3_median, java.lang.String cy3_bruit, java.lang.String cy5_median, java.lang.String cy5_bruit, java.lang.String ratio, java.lang.String bloc, java.lang.String column, java.lang.String row, java.lang.String flag)
Constructs an ElementMap object from several parameters

Method Summary

java.lang.String	getBloc() Bloc in which the oligo is located
java.lang.String	getColumn() Column in Bloc in which the oligo is located
java.lang.String	getCy3_bruit() Cy3 Signal Background of the spot
java.lang.String	getCy3_median() Cy3 Signal of the spot
java.lang.String	getCy5_bruit() Cy5 Signal Background of the spot
java.lang.String	getCy5_median() Cy5 Signal of the spot
java.lang.String	getFlag_str() Flag string of the spot
boolean	getFlag() Flag true or false of the spot
boolean	getIs_adhoc() if this oligo is an adhoc oligo
boolean	getIs_control() if this oligo is an oligo control
boolean	getIs_externe() if this oligo is an external oligo
boolean	getIs_tiling() if this oligo is a tiling oligo
java.lang.String	getOligo_id_str() Oligo ID string object of this ElementMap
int	getOligo_id() ID of Oligo object of this ElementMap
java.lang.String	getRatio() Ratio Signal of the spot
int	getRayon() rayon of the oligo on the Tiff image
java.lang.String	getRow() Row in Bloc in which the oligo is located
java.lang.String	getSymbol() Symbol of Oligo object of this ElementMap
int	getX_coord() X_coord of the oligo on the Tiff image
int	getY_coord() Y_coord of the oligo on the Tiff image
void	set(boolean flag)
void	setBloc(java.lang.String bloc)
void	setColumn(java.lang.String column)
void	setCy3_bruit(java.lang.String cy3_bruit)
void	setCy3_median(java.lang.String cy3_median)
void	setCy5_bruit(java.lang.String cy5_bruit)
void	setCy5_median(java.lang.String cy5_median)
void	setFlag_str(java.lang.String flag_str)
void	setIs_adhoc(boolean is_adhoc)
void	setIs_control(boolean is_control)
void	setIs_externe(boolean is_externe)
void	setIs_tiling(boolean is_tiling)
void	setOligo_id_str(java.lang.String oligo_id_str)
void	setOligo_id(int oligo_id)
void	setRatio(java.lang.String ratio)
void	setRayon(int rayon)
void	setRow(java.lang.String row)
void	setSymbol(java.lang.String symbol)
void	setX_coord(int x_coord)
void	setY_coord(int y_coord)

Methods inherited from class java.lang.Object

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

Field Detail

oligo_id

private int oligo_id

ID of Oligo object of this ElementMap

symbol

private java.lang.String symbol

Symbol of Oligo object of this ElementMap

x_coord

private int x_coord

X_coord of the oligo on the Tiff image

y_coord

private int y_coord

Y_coord of the oligo on the Tiff image

rayon

private int rayon

rayon of the oligo on the Tiff image

is_control

private boolean is_control

if this oligo is an oligo control

is_adhoc

private boolean is_adhoc

if this oligo is an adhoc oligo

is_externe

private boolean is_externe

if this oligo is an external oligo

is_tiling

private boolean is_tiling

if this oligo is a tiling oligo

bloc

private java.lang.String bloc

Bloc in which the oligo is located

column

private java.lang.String column

Column in Bloc in which the oligo is located

row

private java.lang.String row

Row in Bloc in which the oligo is located

cy3_median

private java.lang.String cy3_median

Cy3 Signal of the spot

cy3_bruit

private java.lang.String cy3_bruit

Cy3 Signal Background of the spot

cy5_median

private java.lang.String cy5_median

Cy5 Signal of the spot

cy5_bruit

private java.lang.String cy5_bruit

Cy5 Signal Background of the spot

ratio

private java.lang.String ratio

Ratio Signal of the spot

flag

private boolean flag

Flag true or false of the spot

oligo_id_str

private java.lang.String oligo_id_str

ID String of Oligo object of this ElementMap

flag_str

private java.lang.String flag_str

Flag string of the spot

Constructor Detail

ElementMap

public ElementMap()

Default constructor

ElementMap

public ElementMap(java.lang.String symbol,
                  java.lang.String oid,
                  int x_coord,
                  int y_coord,
                  int rayon,
                  java.lang.String cy3_median,
                  java.lang.String cy3_bruit,
                  java.lang.String cy5_median,
                  java.lang.String cy5_bruit,
                  java.lang.String ratio,
                  java.lang.String bloc,
                  java.lang.String column,
                  java.lang.String row,
                  java.lang.String flag)

Constructs an ElementMap object from several parameters

Parameters:

symbol -

oid - ID of an Oligo Object

x_coord - X coord on microarray

y_coord - Y coord on microarray

rayon - Rayon of spot

cy3_median - Median of cy3 signal

cy3_bruit - Bruit of cy3 signal

cy5_median - Median of cy5 signal

cy5_bruit - Bruit of cy5 signal

ratio - signal ratio from genpix

bloc - Block within array

column - Column within array

row - Row within array

flag - Flag for this spot

Method Detail

getOligo_id

public int getOligo_id()

ID of Oligo object of this ElementMap

setOligo_id

public void setOligo_id(int oligo_id)

getOligo_id_str

public java.lang.String getOligo_id_str()

Oligo ID string object of this ElementMap

setOligo_id_str

public void setOligo_id_str(java.lang.String oligo_id_str)

getSymbol

public java.lang.String getSymbol()

Symbol of Oligo object of this ElementMap

setSymbol

public void setSymbol(java.lang.String symbol)

getX_coord

public int getX_coord()

X_coord of the oligo on the Tiff image

setX_coord

public void setX_coord(int x_coord)

getY_coord

public int getY_coord()

Y_coord of the oligo on the Tiff image

setY_coord

public void setY_coord(int y_coord)

getRayon

public int getRayon()

rayon of the oligo on the Tiff image

setRayon

public void setRayon(int rayon)

getIs_control

public boolean getIs_control()

if this oligo is an oligo control

setIs_control

public void setIs_control(boolean is_control)

getIs_adhoc

public boolean getIs_adhoc()

if this oligo is an adhoc oligo

setIs_adhoc

public void setIs_adhoc(boolean is_adhoc)

getIs_externe

public boolean getIs_externe()

if this oligo is an external oligo

setIs_externe

public void setIs_externe(boolean is_externe)

getIs_tiling

public boolean getIs_tiling()

if this oligo is a tiling oligo

setIs_tiling

public void setIs_tiling(boolean is_tiling)

getCy3_median

public java.lang.String getCy3_median()

Cy3 Signal of the spot

setCy3_median

public void setCy3_median(java.lang.String cy3_median)

getCy3_bruit

public java.lang.String getCy3_bruit()

Cy3 Signal Background of the spot

setCy3_bruit

public void setCy3_bruit(java.lang.String cy3_bruit)

getCy5_median

public java.lang.String getCy5_median()

Cy5 Signal of the spot

setCy5_median

public void setCy5_median(java.lang.String cy5_median)

getCy5_bruit

public java.lang.String getCy5_bruit()

Cy5 Signal Background of the spot

setCy5_bruit

public void setCy5_bruit(java.lang.String cy5_bruit)

getRatio

public java.lang.String getRatio()

Ratio Signal of the spot

setRatio

public void setRatio(java.lang.String ratio)

getBloc

public java.lang.String getBloc()

Bloc in which the oligo is located

setBloc

public void setBloc(java.lang.String bloc)

getRow

public java.lang.String getRow()

Row in Bloc in which the oligo is located

setRow

public void setRow(java.lang.String row)

getColumn

public java.lang.String getColumn()

Column in Bloc in which the oligo is located

setColumn

public void setColumn(java.lang.String column)

getFlag

public boolean getFlag()

Flag true or false of the spot

set

public void set(boolean flag)

getFlag_str

public java.lang.String getFlag_str()

Flag string of the spot

setFlag_str

public void setFlag_str(java.lang.String flag_str)