Class Element

java.lang.Object
  |
  +--Element

public class Element

extends java.lang.Object

This class represents individual array data element corresponding to a spot. It contains the relevant fields from the input data file that are used by the MAExplorer program.

This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government. As a work of the United States Government there is no associated copyright. It is offered as open source software under the Mozilla Public License (version 1.1) subject to the limitations noted in the accompanying LEGAL file.

Version:

$Date: 2002/10/14 19:22:29 $ $Revision: 1.7 $

Author:

P. Lemkin (NCI), B. Stephens(SAIC), G. Thornwall (SAIC), NCI-Frederick, Frederick, MD

See Also:

MAExplorer Home

Field Summary

(package private) java.lang.String	cloneID GIPO data
(package private) java.lang.String	dbEst3 GIPO data
(package private) java.lang.String	dbEst5 GIPO data
(package private) java.lang.String	detValue quant data Affy feature - Spot Detection Value (Det p-value)
(package private) java.lang.String	diffCall quant data Affy feature - "Diff call" is PM, MM, AM
(package private) java.lang.String	field GIPO data
(package private) java.lang.String	foldChange [Future] quant data Affy feature - "Fold change"
(package private) java.lang.String	genBankAcc GIPO data
(package private) java.lang.String	genBankAcc3 GIPO data
(package private) java.lang.String	genBankAcc5 GIPO data
(package private) java.lang.String	geneName GIPO data
(package private) java.lang.String	grid GIPO data
(package private) java.lang.String	grid_col GIPO data
(package private) java.lang.String	grid_row GIPO data
(package private) java.lang.String	identifier generic Genomic ID
(package private) int	iLocation int value of Location
(package private) java.lang.String	location either spotNbr or Location value
(package private) java.lang.String	locusLinkID GIPO data
(package private) java.lang.String	NAME_GRC GIPO data
(package private) java.lang.String	plate GIPO data
(package private) java.lang.String	plate_col GIPO data
(package private) java.lang.String	plate_row GIPO data
(package private) java.lang.String	qualCheck GIPO data
(package private) java.lang.String	qualCheck1 Quantification data
(package private) java.lang.String	qualCheck2 Quantification data
(package private) java.lang.String	rawBkgrd Quantification data
(package private) java.lang.String	rawBkgrd1 Quantification data
(package private) java.lang.String	rawBkgrd2 Quantification data
(package private) java.lang.String	rawIntensity Quantification data
(package private) java.lang.String	rawIntensity1 Quantification data
(package private) java.lang.String	rawIntensity2 Quantification data
(package private) java.lang.String	spotNbr sequential id for this Element
(package private) java.lang.String	swissProtID GIPO data
(package private) java.lang.String	unigene_cluster_ID GIPO data
(package private) java.lang.String	unigene_cluster_name GIPO data

Constructor Summary

Element()
Element() - constructor for empty element Note: strings are null!

Methods inherited from class java.lang.Object

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

Field Detail

iLocation

int iLocation

int value of Location

spotNbr

java.lang.String spotNbr

sequential id for this Element

location

java.lang.String location

either spotNbr or Location value

identifier

java.lang.String identifier

generic Genomic ID

field

java.lang.String field

GIPO data

grid

java.lang.String grid

GIPO data

grid_col

java.lang.String grid_col

GIPO data

grid_row

java.lang.String grid_row

GIPO data

NAME_GRC

java.lang.String NAME_GRC

GIPO data

plate

java.lang.String plate

GIPO data

plate_col

java.lang.String plate_col

GIPO data

plate_row

java.lang.String plate_row

GIPO data

qualCheck

java.lang.String qualCheck

GIPO data

cloneID

java.lang.String cloneID

GIPO data

geneName

java.lang.String geneName

GIPO data

unigene_cluster_ID

java.lang.String unigene_cluster_ID

GIPO data

unigene_cluster_name

java.lang.String unigene_cluster_name

GIPO data

genBankAcc

java.lang.String genBankAcc

GIPO data

genBankAcc3

java.lang.String genBankAcc3

GIPO data

genBankAcc5

java.lang.String genBankAcc5

GIPO data

dbEst3

java.lang.String dbEst3

GIPO data

dbEst5

java.lang.String dbEst5

GIPO data

swissProtID

java.lang.String swissProtID

GIPO data

locusLinkID

java.lang.String locusLinkID

GIPO data

rawIntensity

java.lang.String rawIntensity

Quantification data

rawIntensity1

java.lang.String rawIntensity1

Quantification data

rawIntensity2

java.lang.String rawIntensity2

Quantification data

rawBkgrd

java.lang.String rawBkgrd

Quantification data

rawBkgrd1

java.lang.String rawBkgrd1

Quantification data

rawBkgrd2

java.lang.String rawBkgrd2

Quantification data

qualCheck1

java.lang.String qualCheck1

Quantification data

qualCheck2

java.lang.String qualCheck2

Quantification data

detValue

java.lang.String detValue

quant data Affy feature - Spot Detection Value (Det p-value)

diffCall

java.lang.String diffCall

quant data Affy feature - "Diff call" is PM, MM, AM

foldChange

java.lang.String foldChange

[Future] quant data Affy feature - "Fold change"

Constructor Detail

Element

public Element()

Element() - constructor for empty element Note: strings are null!