object.microarray
Class Feature

java.lang.Object
  object.microarray.Feature

All Implemented Interfaces:

java.io.Serializable

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

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

See Also:

Serialized Form

Field Summary

private java.lang.String	average Average of feature
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_norm Flag of feature
private java.lang.String	flag_str Flag string of the spot
private java.lang.String	geo_id_ref ID_REF for GEO submission
private java.util.Hashtable	hashScore Hashtable of score for this feature
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 java.lang.String	logratio LogRatio of feature
private java.lang.String	name Name of Oligo object of this Feature
private int	oligo_id ID of Oligo object of this Feature
private java.lang.String	oligo_id_str ID String of Oligo object of this Feature
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	shortName shortName of Oligo object of this Feature
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

Feature()
Default constructor

Feature(java.lang.String geo_id_ref, java.lang.String name, 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 Feature object from several parameters

Method Summary

java.lang.String	getAverage()
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_norm()
java.lang.String	getFlag_str() Flag string of the spot
boolean	getFlag() Flag true or false of the spot
java.lang.String	getGeo_id_ref() ID_ref for GEO submission
java.util.Hashtable	getHashScore()
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	getLink(int x, int y, int r)
java.lang.String	getLogratio()
java.lang.String	getName() Name of Oligo object of this Feature
java.lang.String	getOligo_id_str() Oligo ID string object of this Feature
int	getOligo_id() ID of Oligo object of this Feature
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	getShortName() Short Name of Oligo object of this Feature
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	setAverage(java.lang.String average)
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_norm(java.lang.String flag_norm)
void	setFlag_str(java.lang.String flag_str)
void	setGeo_id_ref(java.lang.String geo_id_ref)
void	setHashScore(java.util.Hashtable hashScore)
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	setLogratio(java.lang.String logratio)
void	setName(java.lang.String name)
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	setShortName(java.lang.String shortName)
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 Feature

name

private java.lang.String name

Name of Oligo object of this Feature

shortName

private java.lang.String shortName

shortName of Oligo object of this Feature

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 Feature

flag_str

private java.lang.String flag_str

Flag string of the spot

geo_id_ref

private java.lang.String geo_id_ref

ID_REF for GEO submission

average

private java.lang.String average

Average of feature

logratio

private java.lang.String logratio

LogRatio of feature

flag_norm

private java.lang.String flag_norm

Flag of feature

hashScore

private java.util.Hashtable hashScore

Hashtable of score for this feature

Constructor Detail

Feature

public Feature()

Default constructor

Feature

public Feature(java.lang.String geo_id_ref,
               java.lang.String name,
               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 Feature object from several parameters

Parameters:

name -

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 genepix

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 Feature

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 Feature

setOligo_id_str

public void setOligo_id_str(java.lang.String oligo_id_str)

getName

public java.lang.String getName()

Name of Oligo object of this Feature

setName

public void setName(java.lang.String name)

getShortName

public java.lang.String getShortName()

Short Name of Oligo object of this Feature

setShortName

public void setShortName(java.lang.String shortName)

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)

getGeo_id_ref

public java.lang.String getGeo_id_ref()

ID_ref for GEO submission

setGeo_id_ref

public void setGeo_id_ref(java.lang.String geo_id_ref)

getAverage

public java.lang.String getAverage()

setAverage

public void setAverage(java.lang.String average)

getLogratio

public java.lang.String getLogratio()

setLogratio

public void setLogratio(java.lang.String logratio)

getFlag_norm

public java.lang.String getFlag_norm()

setFlag_norm

public void setFlag_norm(java.lang.String flag_norm)

getHashScore

public java.util.Hashtable getHashScore()

setHashScore

public void setHashScore(java.util.Hashtable hashScore)

getLink

public java.lang.String getLink(int x,
                                int y,
                                int r)