Class Spot

java.lang.Object
  Spot

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.util.EventListener

public class Spot
extends java.lang.Object
implements java.awt.event.ActionListener, java.awt.event.WindowListener

Class Spot contains the spot structure for measured spots.

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 Flicker Mozilla and Legal files are available on http://open2dprot.sourceforge.net/Flicker

Version:

$Date$ $Revision$

Author:

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

See Also:

Flicker Home

Field Summary

(package private) float	area spot area in pixels
(package private) float	bkgrd total spot mean background density
private boolean	changedFlag edited the spot flag
(package private) int	circleRadius he radius of the circlular mask
(package private) float	density total density uncorrected for background computed as the sum of the gray value or calibrated gray value (i.e.
(package private) float	densPrime total density corrected for background by computed as: densPrime = (density - mnBkgrd*area)
(package private) float	dMax spot MAX OD
(package private) float	dMaxBkgrd background for spot MAX OD or gray value
(package private) float	dMin spot MIN OD
(package private) float	dMinBkgrd background for spot MIN OD or gray value
private static java.awt.Frame	fBoth Frame to create and popup when you edit
static FileIO	fio FileIO utilities
private static Flicker	flk instance of Flicker
static java.lang.String[]	fNames names of the spot fields
private static java.awt.Frame	fOne Frame to create and popup when you edit
(package private) java.lang.String	id Optional associated identifier string if not null.
static int	idxID index of "id" field in fNames table.
(package private) boolean	isCalibFlag measurements are in calibrated OD rather than grayscale
(package private) float	mnBkgrd mean spot mean background density
(package private) float	mnDens mean density
(package private) float	mnDensPrime mean density corrected for background (mnDensPrime - mnBkgrd)
(package private) java.lang.String	name Optional associated protein string if not null.
(package private) int	nbr measurement number of spot unique to the associated gel
(package private) int	nCirMask circular mask diameter = 2*circleRadius+1
(package private) int	nGel Gel# (1 or 2) for "left" or "right" image.
static int	nRows # of names for the spot fields
(package private) static int	POPUP_HEIGHT default frame size height of popup
(package private) static int	POPUP_WIDTH default frame size width of popup
int	preferredHeight preferred canvas height
int	preferredWidth preferred canvas width
private Spot	s1 Left Spot 1 if editing both spots
private Spot	s2 Right Spot 2 if editing both spots
private static java.awt.TextField[][]	spotTable spot Editable table [nRows][2]
private static java.awt.TextField[][]	spotTableBoth spot Editable table [nRows][3] that handles spots in s1 [1] and spots in s2 [2].
private java.awt.Label	statusLabel status Label
(package private) float	totDens total density over the measurement area
(package private) boolean	useTotDensityFlag measurements total density else mean values
private static Util	util misc utility methods
(package private) int	xB background x centroid
(package private) int	xC spot X centroid
(package private) int	yB background Y centroid
(package private) int	yC spot Y centroid

Constructor Summary

Spot()
Spot() - Constructor for new Spot

Spot(Flicker flkS)
Spot() - setup Spot part of the database

Spot(int nGel, int nbr, java.lang.String id, java.lang.String name, int nCirMask, int circleRadius, int xC, int yC, int xB, int yB, float area, boolean isCalibFlag, boolean useTotDensityFlag, float density, float densPrime, float bkgrd, float mnDens, float totDens, float mnDensPrime, float mnBkgrd, float dMax, float dMin, float dMaxBkgrd, float dMinBkgrd)
Spot() - Constructor for new Spot with data

Method Summary

void	actionPerformed(java.awt.event.ActionEvent e) actionPerformed() - Handle Control panel button clicks
void	close() close() - close this popup and reset flags if needed [TODO] If they edited the calibration and peak calibration table, and they did not save the calibration (i.e.
java.lang.String	cvSpot2Str(java.lang.String imageName, java.lang.String unitsAbbrev) cvSpot2Str() - convert spot to printable string
java.lang.String	getID() getID() - get the spot ID
java.awt.Dimension	getMinimumSize() getMinimumSize() - get the minimum preferred size
java.awt.Dimension	getPreferredSize() getPreferredSize() - get the preferred size
java.lang.String	getValBySpotFieldName(java.lang.String sName) getValBySpotFieldName() - get spot value string by spot field name
static java.lang.String	listPairedSpotListDataTabDelim(boolean normByMeanSpotListFlag) listPairedSpotListDataTabDelim() - generate a tab-delimited string table of the paired spots (by matching spot id's) in the spot list.
static java.lang.String	listSpotListData(java.lang.String imageName, java.lang.String units, Spot[] spotList, int nSpots) listSpotListData() - generate a string list of the spots in the spot list
static java.lang.String	listSpotListDataTabDelim(java.lang.String imageName, java.lang.String unitsAbbrev, Spot[] spotList, int nSpots) listSpotListDataTabDelim() - generate a tab-delimited string table of of the spots in the spot list.
boolean	popupSpotEdit(boolean editOnlyIDflag) popupSpotEdit() - popup a spot editing function to change the spot.
boolean	popupSpotEditBoth(Spot s1, Spot s2, boolean editOnlyIDflag) popupSpotEditBoth() - popup a spot editing function to let you edit two selected (putatively paired) spots together Edit the data in 3 columns with the field name on the left column the left image data in the middle column and the right image data in the right column.
void	positionWindow(java.awt.Frame f) positionWindow() - position window on the screen
(package private) static Spot[]	readState(java.lang.String gelFile, java.lang.String iName) readState() - Read spotList[] "spt/.spt" file
static boolean	rmvSpotListFile(java.lang.String gelFile, java.lang.String iName) rmvSpotListFile() - clear the .spt file from the spt/ directory by moving the spt/.spt file into spt/.spt.bkup andclearing the .bkup file if it previously existed first.
void	set(int nGel, int nbr, java.lang.String id, java.lang.String name, int nCirMask, int circleRadius, int xC, int yC, int xB, int yB, float area, boolean isCalibFlag, boolean useTotDensityFlag, float density, float densPrime, float bkgrd, float mnDens, float totDens, float mnDensPrime, float mnBkgrd, float dMax, float dMin, float dMaxBkgrd, float dMinBkgrd) set() - set the data for a spot with new data
void	setID(java.lang.String id) setID() - set the spot ID
void	setStatusMsg(java.lang.String msg) setStatusMsg() - set the status msg
void	setStatusMsg(java.lang.String msg, java.awt.Color color) setStatusMsg() - set the status msg
private boolean	updateBothSpotsFromEditedSpotTable() updateBothSpotsFromEditedSpotTable() - set both spots from the spotTableBoth table data
private boolean	updateSpotFromEditedSpotTable() updateSpotFromEditedSpotTable() - set the spot from the table data
void	windowActivated(java.awt.event.WindowEvent e)
void	windowClosed(java.awt.event.WindowEvent e)
void	windowClosing(java.awt.event.WindowEvent e) windowClosing() - close down the window.
void	windowDeactivated(java.awt.event.WindowEvent e)
void	windowDeiconified(java.awt.event.WindowEvent e)
void	windowIconified(java.awt.event.WindowEvent e)
void	windowOpened(java.awt.event.WindowEvent e)
(package private) static boolean	writeState(java.lang.String gelFile, java.lang.String iName, Spot[] spotList, int nSpots) writeState() - Write the spotlist[] to "spt/.spt" file

Methods inherited from class java.lang.Object

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

Field Detail

flk

private static Flicker flk

instance of Flicker

fio

public static FileIO fio

FileIO utilities

util

private static Util util

misc utility methods

POPUP_WIDTH

static final int POPUP_WIDTH

default frame size width of popup

See Also:

Constant Field Values

POPUP_HEIGHT

static final int POPUP_HEIGHT

default frame size height of popup

See Also:

Constant Field Values

preferredHeight

public int preferredHeight

preferred canvas height

preferredWidth

public int preferredWidth

preferred canvas width

nGel

int nGel

Gel# (1 or 2) for "left" or "right" image.

nbr

int nbr

measurement number of spot unique to the associated gel

id

java.lang.String id

Optional associated identifier string if not null.

name

java.lang.String name

Optional associated protein string if not null.

nCirMask

int nCirMask

circular mask diameter = 2*circleRadius+1

circleRadius

int circleRadius

he radius of the circlular mask

xC

int xC

spot X centroid

yC

int yC

spot Y centroid

xB

int xB

background x centroid

yB

int yB

background Y centroid

area

float area

spot area in pixels

isCalibFlag

boolean isCalibFlag

measurements are in calibrated OD rather than grayscale

useTotDensityFlag

boolean useTotDensityFlag

measurements total density else mean values

density

float density

total density uncorrected for background computed as the sum of the gray value or calibrated gray value (i.e. OD?)

densPrime

float densPrime

total density corrected for background by computed as: densPrime = (density - mnBkgrd*area)

bkgrd

float bkgrd

total spot mean background density

mnDens

float mnDens

mean density

totDens

float totDens

total density over the measurement area

mnDensPrime

float mnDensPrime

mean density corrected for background (mnDensPrime - mnBkgrd)

mnBkgrd

float mnBkgrd

mean spot mean background density

dMax

float dMax

spot MAX OD

dMin

float dMin

spot MIN OD

dMaxBkgrd

float dMaxBkgrd

background for spot MAX OD or gray value

dMinBkgrd

float dMinBkgrd

background for spot MIN OD or gray value

fOne

private static java.awt.Frame fOne

Frame to create and popup when you edit

fBoth

private static java.awt.Frame fBoth

Frame to create and popup when you edit

fNames

public static java.lang.String[] fNames

names of the spot fields

idxID

public static int idxID

index of "id" field in fNames table. Edit if fName[] list changes

nRows

public static int nRows

# of names for the spot fields

spotTable

private static java.awt.TextField[][] spotTable

spot Editable table [nRows][2]

spotTableBoth

private static java.awt.TextField[][] spotTableBoth

spot Editable table [nRows][3] that handles spots in s1 [1] and spots in s2 [2].

s1

private Spot s1

Left Spot 1 if editing both spots

s2

private Spot s2

Right Spot 2 if editing both spots

statusLabel

private java.awt.Label statusLabel

status Label

changedFlag

private boolean changedFlag

edited the spot flag

Constructor Detail

Spot

public Spot(Flicker flkS)

Spot() - setup Spot part of the database

Spot

public Spot()

Spot() - Constructor for new Spot

Spot

public Spot(int nGel,
            int nbr,
            java.lang.String id,
            java.lang.String name,
            int nCirMask,
            int circleRadius,
            int xC,
            int yC,
            int xB,
            int yB,
            float area,
            boolean isCalibFlag,
            boolean useTotDensityFlag,
            float density,
            float densPrime,
            float bkgrd,
            float mnDens,
            float totDens,
            float mnDensPrime,
            float mnBkgrd,
            float dMax,
            float dMin,
            float dMaxBkgrd,
            float dMinBkgrd)

Spot() - Constructor for new Spot with data

Parameters:

nGel - is the Gel# (1 or 2) rof "left" or "right" image.

nbr - is measurement number of spot unique to the associated gel

id - is the optional associated identifier string if not null.

name - is the optional associated protein name string if not null.

nCirMask - is the circular mask diameter

circleRadius - is the radius of the circlular mask

xC - is the spot X centroid

yC - is the spot Y centroid

xB - is background x centroid

yB - is background Y centroid

area - is spot area in pixels (float so possibly scaled)

isCalibFlag - is measurements are in calibrated OD rather than grayscale

useTotDensityFlag - measurements total density else mean values

density - is the total density uncorrected for background computed as the sum of the gray value or calibrated gray value (i.e. OD?)

densPrime - is the total density corrected for background by computed as: densPrime = (density - mnBkgrd*area)

bkgrd - is the total spot mean background density

mnDens - is the mean density

totDens - is the total density over the measurement area

mnDensPrime - is mean density corrected for background computed as (mnDensPrime - mnBkgrd)

mnBkgrd - is the mean spot mean background density

dMax - is spot MAX OD

dMin - is spot MIN OD

dMaxBkgrd - background for spot MAX OD or gray value

dMinBkgrd - background for spot MIN OD or gray value

Method Detail

set

public void set(int nGel,
                int nbr,
                java.lang.String id,
                java.lang.String name,
                int nCirMask,
                int circleRadius,
                int xC,
                int yC,
                int xB,
                int yB,
                float area,
                boolean isCalibFlag,
                boolean useTotDensityFlag,
                float density,
                float densPrime,
                float bkgrd,
                float mnDens,
                float totDens,
                float mnDensPrime,
                float mnBkgrd,
                float dMax,
                float dMin,
                float dMaxBkgrd,
                float dMinBkgrd)

set() - set the data for a spot with new data

Parameters:

nGel - is the Gel# (1 or 2) rof "left" or "right" image.

nbr - is measurement number of spot unique to the associated gel

id - is the optional associated identifier string if not null.

name - is the optional associated protein name string if not null.

nCirMask - is the circular mask diameter

circleRadius - is the radius of the circlular mask

xC - is the spot X centroid

yC - is the spot Y centroid

xB - is background x centroid

yB - is background Y centroid

area - is spot area in pixels (float so possibly scaled)

isCalibFlag - is measurements are in calibrated OD rather than grayscale

useTotDensityFlag - measurements total density else mean values

density - is the total density uncorrected for background computed as the sum of the gray value or calibrated gray value (i.e. OD?)

densPrime - is the total density corrected for background by computed as: densPrime = (density - mnBkgrd*area)

bkgrd - is the total spot mean background density

mnDens - is the mean density

totDens - is the total density over the measurement area

mnDensPrime - is mean density corrected for background computed as (mnDensPrime - mnBkgrd)

mnBkgrd - is the mean spot mean background density

dMax - is spot MAX OD

dMin - is spot MIN OD

dMaxBkgrd - background for spot MAX OD or gray value

dMinBkgrd - background for spot MIN OD or gray value

getID

public java.lang.String getID()

getID() - get the spot ID

Returns:

the spot id

setID

public void setID(java.lang.String id)

setID() - set the spot ID

Parameters:

the - spot id

readState

static Spot[] readState(java.lang.String gelFile,
                        java.lang.String iName)

readState() - Read spotList[] "spt/.spt" file

Parameters:

gelFile - is the file base name. We strip off the image type and add ".spt"

iName - of the image to read (e.g., "I1", or "I2")

Returns:

spot list array if succeed, else null

writeState

static boolean writeState(java.lang.String gelFile,
                          java.lang.String iName,
                          Spot[] spotList,
                          int nSpots)

writeState() - Write the spotlist[] to "spt/.spt" file

Parameters:

gelFile - is the file base name. We strip off the image type and add ".spt"

iName - of the image to read (e.g., "I1", or "I2")

spotList - is list of spots to write out

sBuf - is the string buffer to write to.

Returns:

true if succeed

rmvSpotListFile

public static boolean rmvSpotListFile(java.lang.String gelFile,
                                      java.lang.String iName)

rmvSpotListFile() - clear the .spt file from the spt/ directory by moving the spt/.spt file into spt/.spt.bkup andclearing the .bkup file if it previously existed first.

Parameters:

gelFile - is the file base name. We strip off the image type and add ".spt"

iName - of the image to remove (e.g., "I1", or "I2")

Returns:

true if succeed

cvSpot2Str

public java.lang.String cvSpot2Str(java.lang.String imageName,
                                   java.lang.String unitsAbbrev)

cvSpot2Str() - convert spot to printable string

Parameters:

imageName - is image name

unitsAbbrev - is name of units abbreviation else "gray-scale"

Returns:

spot as string

listSpotListData

public static java.lang.String listSpotListData(java.lang.String imageName,
                                                java.lang.String units,
                                                Spot[] spotList,
                                                int nSpots)

listSpotListData() - generate a string list of the spots in the spot list

Parameters:

imageName - is image name

units - is name of units else "gray-scale"

spotList - is list of spots to convert

nspots - to convert

Returns:

spot as string

listSpotListDataTabDelim

public static java.lang.String listSpotListDataTabDelim(java.lang.String imageName,
                                                        java.lang.String unitsAbbrev,
                                                        Spot[] spotList,
                                                        int nSpots)

listSpotListDataTabDelim() - generate a tab-delimited string table of of the spots in the spot list. This could be imported into Excel

Parameters:

imageName - is image name

unitsAbbrev - is name of units abbreviation else "gray-scale"

spotList - is list of spots to convert

nspots - to convert

Returns:

spot as string

listPairedSpotListDataTabDelim

public static java.lang.String listPairedSpotListDataTabDelim(boolean normByMeanSpotListFlag)

listPairedSpotListDataTabDelim() - generate a tab-delimited string table of the paired spots (by matching spot id's) in the spot list. Note:

  1. Both spot list must be measured with either Total or Mean densities,
  2. Both spot lists must have the same calibration abbreviation units
  3. Both spots that are paired must have the same annotation id spelling
     including case.

This could be imported into Excel

Parameters:

normByMeanSpotListFlag - normalize by the mean spot value of spots in each of the corresponding spot lists.

Returns:

the table as string, else null if no data

getPreferredSize

public java.awt.Dimension getPreferredSize()

getPreferredSize() - get the preferred size

Returns:

window size

getMinimumSize

public java.awt.Dimension getMinimumSize()

getMinimumSize() - get the minimum preferred size

Returns:

window size

positionWindow

public void positionWindow(java.awt.Frame f)

positionWindow() - position window on the screen

popupSpotEdit

public boolean popupSpotEdit(boolean editOnlyIDflag)

popupSpotEdit() - popup a spot editing function to change the spot.

Parameters:

editOnlyIDflag - if only want to edit/assign the spot id

Returns:

true if any fields changed.

popupSpotEditBoth

public boolean popupSpotEditBoth(Spot s1,
                                 Spot s2,
                                 boolean editOnlyIDflag)

popupSpotEditBoth() - popup a spot editing function to let you edit two selected (putatively paired) spots together Edit the data in 3 columns with the field name on the left column the left image data in the middle column and the right image data in the right column.

Parameters:

s1 - is first spot

s2 - is second spot

editOnlyIDflag - if only want to edit/assign the spot id

Returns:

true if any fields changed.

setStatusMsg

public void setStatusMsg(java.lang.String msg)

setStatusMsg() - set the status msg

Parameters:

msg - is the status window msg

setStatusMsg

public void setStatusMsg(java.lang.String msg,
                         java.awt.Color color)

setStatusMsg() - set the status msg

Parameters:

msg - is the status window msg

color - to draw it

getValBySpotFieldName

public java.lang.String getValBySpotFieldName(java.lang.String sName)

getValBySpotFieldName() - get spot value string by spot field name

Parameters:

name - of spot field

Returns:

null if not found, else string value

updateSpotFromEditedSpotTable

private boolean updateSpotFromEditedSpotTable()

updateSpotFromEditedSpotTable() - set the spot from the table data

updateBothSpotsFromEditedSpotTable

private boolean updateBothSpotsFromEditedSpotTable()

updateBothSpotsFromEditedSpotTable() - set both spots from the spotTableBoth table data

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent e)

actionPerformed() - Handle Control panel button clicks

Specified by:

actionPerformed in interface java.awt.event.ActionListener

Parameters:

e - is ActionEvent for buttons in control panel

close

public void close()

close() - close this popup and reset flags if needed [TODO] If they edited the calibration and peak calibration table, and they did not save the calibration (i.e. calibChangedFlag is true), then ask them here and save it if they say yes. If not, then restore the previous calibration.

windowClosing

public void windowClosing(java.awt.event.WindowEvent e)

windowClosing() - close down the window.

Specified by:

windowClosing in interface java.awt.event.WindowListener

Parameters:

e - is window closing event

See Also:

close()

windowOpened

public void windowOpened(java.awt.event.WindowEvent e)

Specified by:

windowOpened in interface java.awt.event.WindowListener

windowActivated

public void windowActivated(java.awt.event.WindowEvent e)

Specified by:

windowActivated in interface java.awt.event.WindowListener

windowClosed

public void windowClosed(java.awt.event.WindowEvent e)

Specified by:

windowClosed in interface java.awt.event.WindowListener

windowDeactivated

public void windowDeactivated(java.awt.event.WindowEvent e)

Specified by:

windowDeactivated in interface java.awt.event.WindowListener

windowDeiconified

public void windowDeiconified(java.awt.event.WindowEvent e)

Specified by:

windowDeiconified in interface java.awt.event.WindowListener

windowIconified

public void windowIconified(java.awt.event.WindowEvent e)

Specified by:

windowIconified in interface java.awt.event.WindowListener