Class SpotData

java.lang.Object
  |
  +--SpotData

class SpotData

extends java.lang.Object

The SpotData class is used as a static object to hold gene (HP-X,HP-Y), (f1,f2) spot quantified data and (x,y) coordiantes for a particular hybridized sample HP or pairs of samples (HP-X and HP-Y). Data may be assembled here from various sources but then used as a single object.

Note: This implements a type of "gather" method so that users of this data have what they need for further computations in one structure.

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. This notice must be included with the code. The MAExplorer Mozilla and Legal files are available on http://maexplorer.sourceforge.net/.

Version:

$Date: 2002/10/14 20:44:22 $ $Revision: $

Author:

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

See Also:

MAExplorer Home

Field Summary

(package private) static int	gid1S GridCoords gid of spot 1
(package private) static int	gid2S GridCoords gid of spot 2
(package private) static int	gidS GridCoords gid of a spot
private static MAExplorer	mae link to global MAExplorer instance
(package private) static MaHybridSample	ms HP where this data came from
(package private) static float	tot1S total bkgrd corrected intensity of a spot
(package private) static float	tot2S total bkgrd corrected intensity of a spot
(package private) static float	totS total bkgrd corrected intensity of a spot
(package private) static java.awt.Point	xy1S X,Y Centroid of spot 1
(package private) static java.awt.Point	xy2S X,Y Centroid of spot 2
(package private) static java.awt.Point	xyS X,Y Centroid of a spot

Constructor Summary

(package private)

SpotData(MAExplorer mae) SpotData() - constructor to capture mae.

Method Summary

(package private) static void	setSpotData(MaHybridSample msS, int x, int y, int gid, float tot) setSpotData() - set the default STATIC spot data by (x,y).
(package private) static void	setSpotData(MaHybridSample msS, java.awt.Point xy, int gid, float tot) setSpotData() - set the default STATIC spot data by Point xy.
(package private) static void	setSpotData1(MaHybridSample msS, java.awt.Point xy, int gid, float tot) setSpotData1() - set the default STATIC spot data by Point xy.
(package private) static void	setSpotData2(MaHybridSample msS, java.awt.Point xy, int gid, float tot) setSpotData2() - set the default STATIC spot data by Point xy.

Methods inherited from class java.lang.Object

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

Field Detail

mae

private static MAExplorer mae

link to global MAExplorer instance

ms

static MaHybridSample ms

HP where this data came from

xyS

static java.awt.Point xyS

X,Y Centroid of a spot

xy1S

static java.awt.Point xy1S

X,Y Centroid of spot 1

xy2S

static java.awt.Point xy2S

X,Y Centroid of spot 2

gidS

static int gidS

GridCoords gid of a spot

gid1S

static int gid1S

GridCoords gid of spot 1

gid2S

static int gid2S

GridCoords gid of spot 2

totS

static float totS

total bkgrd corrected intensity of a spot

tot1S

static float tot1S

total bkgrd corrected intensity of a spot

tot2S

static float tot2S

total bkgrd corrected intensity of a spot

Constructor Detail

SpotData

SpotData(MAExplorer mae)

SpotData() - constructor to capture mae.

Parameters:

mae - is instance of MAExplorer

Method Detail

setSpotData

static void setSpotData(MaHybridSample msS,
                        int x,
                        int y,
                        int gid,
                        float tot)

setSpotData() - set the default STATIC spot data by (x,y).

Parameters:

maS - sample to use

x - is X coordinate

y - is Y coordinate

gid - is Grid Index

tot - is raw intensity

setSpotData

static void setSpotData(MaHybridSample msS,
                        java.awt.Point xy,
                        int gid,
                        float tot)

setSpotData() - set the default STATIC spot data by Point xy.

Parameters:

maS - sample to use

xy - is Point X,Y coordinate

gid - is Grid Index

tot - is raw intensity

setSpotData1

static void setSpotData1(MaHybridSample msS,
                         java.awt.Point xy,
                         int gid,
                         float tot)

setSpotData1() - set the default STATIC spot data by Point xy.

Parameters:

maS - sample to use

xy - is Point X,Y coordinate

gid - is Grid Index

tot - is channel 1 raw intensity

setSpotData2

static void setSpotData2(MaHybridSample msS,
                         java.awt.Point xy,
                         int gid,
                         float tot)

setSpotData2() - set the default STATIC spot data by Point xy.

Parameters:

maS - sample to use

xy - is Point X,Y coordinate

gid - is Grid Index

tot - is channel 2 raw intensity