Serialized Form

Class Draw2DprotPlot implements Serializable

Serialized Fields

prp

ProtPlot prp

instance of ProtPlot

rd

ReadPRP rd

instance of ReadPRP

fil

Filter fil

instance of Filter

spp

ShowScatterPlotPopup spp

instance of ShowScatterPlotPopup if the parent, else null

util

UtilPRP util

instance of UtilPRP

preferredHeight

int preferredHeight

target Size for selecting a line

preferredWidth

int preferredWidth

target Size for selecting a line

iWidth

int iWidth

iHeight

int iHeight

normFont

java.awt.Font normFont

The normal font

titleFont

java.awt.Font titleFont

The title font

nPointsMax

int nPointsMax

maximum drawing list size. Set when going to draw

xDataScatterPlot

float[] xDataScatterPlot

X Coords [0:nPointsMax-1] used for computing ratios when clicking

yDataScatterPlot

float[] yDataScatterPlot

Y Coord [0:nPointsMax-1] used for computing ratios when clicking

xPlotted

int[] xPlotted

X Coord [0:nPointsMax-1] for clicking on point in list

yPlotted

int[] yPlotted

Y Coord [0:nPointsMax-1] for clicking on point in list

nPointsPlotted

int nPointsPlotted

# points plotted after data is filtered

cvPrecision

int cvPrecision

vertCaption

java.lang.String vertCaption

horizCaption

java.lang.String horizCaption

title

java.lang.String title

topTitle1

java.lang.String topTitle1

topTitle2

java.lang.String topTitle2

topTitle3

java.lang.String topTitle3

topTitle4

java.lang.String topTitle4

lowerTitle1

java.lang.String lowerTitle1

lowerTitle2

java.lang.String lowerTitle2

info1

java.lang.String info1

info2

java.lang.String info2

info3

java.lang.String info3

info4

java.lang.String info4

info5

java.lang.String info5

info6

java.lang.String info6

aText

java.lang.String aText

xText

int xText

yText

int yText

scaleX

double scaleX

scaleY

double scaleY

minX

double minX

range set in initial call

maxX

double maxX

range set in initial call

minY

double minY

range set in initial call

maxY

double maxY

range set in initial call

minXscroll

double minXscroll

range set by ShowPlotPopup scrollers

minYscroll

double minYscroll

range set by ShowPlotPopup scrollers

maxXscroll

double maxXscroll

range set by ShowPlotPopup scrollers

maxYscroll

double maxYscroll

range set by ShowPlotPopup scrollers

logScalingFlag

boolean logScalingFlag

Linear(false)/Log(true)

xScale

float xScale

slope for xList to xPnt

yScale

float yScale

slope for yList to yPnt

xBase

float xBase

baseline for xList to xPnt

yBase

float yBase

baseline for yList to yPnt

xOffset

int xOffset

yOffset

int yOffset

xRange

float xRange

yRange

float yRange

xLeft

int xLeft

xRight

int xRight

scaleXplot

float scaleXplot

scaleYplot

float scaleYplot

logScaleY

float logScaleY

logScaleX

float logScaleX

scale

int scale

radius

int radius

leftTextX

int leftTextX

yTop

int yTop

iCurMPid

int iCurMPid

xcurProtein

int xcurProtein

current protein if defined

ycurProtein

int ycurProtein

current protein if defined

sMinX

java.lang.String sMinX

sMaxX

java.lang.String sMaxX

sMinY

java.lang.String sMinY

sMaxY

java.lang.String sMaxY

curProteinColor

java.awt.Color curProteinColor

okColor

java.awt.Color okColor

notOkColor

java.awt.Color notOkColor

pointColor

java.awt.Color pointColor

xPnt

int xPnt

xList[0:prp.nMpidSamples-1] data mapped to int

yPnt

int yPnt

yList[0:prp.nMpidSamples-1] data mapped to int

iBest

int iBest

Best index of spot closest to where clicked with mouse

eDiff

float eDiff

eDiffBest

float eDiffBest

img

java.awt.Image img

[TODO] buffered spot image. This gets updated 1. if useFilterFlag, useExprFlag changes 2. if filtering and the Filter or tissue bits change.

drawIntoImageFlag

boolean drawIntoImageFlag

set if draw clustergram to GIF file

oGifFileName

java.lang.String oGifFileName

GIF output file if used

Class DrawProtScatterPlot implements Serializable

Serialized Fields

prp

ProtPlot prp

instance of ProtPlot

rd

ReadPRP rd

instance of ReadPRP of current sample

rdX

ReadPRP rdX

instance of ReadPRP of ratio sample X

rdY

ReadPRP rdY

instance of ReadPRP of ratio sample Y

spp

ShowScatterPlotPopup spp

instance of ShowScatterPlotPopup

util

UtilPRP util

instance of UtilPRP

prevBestMPID

int prevBestMPID

previus best mPid of protein selected by mouse motion or clicking

showAssocWebPageFlag

boolean showAssocWebPageFlag

flag to allow popup web access to associated protein database

maxPoints

int maxPoints

max # points allocated for drawing arrays

Class ExprProfileCanvas implements Serializable

Serialized Fields

prp

ProtPlot prp

instance of ProtPlot so we can clear flags indicating the user did a manual quit()

util

UtilPRP util

instance of UtilPRP

ep

ExprProfile ep

expression profile for mPid

preferredHeight

int preferredHeight

preferred canvas height size

preferredWidth

int preferredWidth

preferred canvas width size

xCursor

int xCursor

event handler mouse X cursor coordinates

yCursor

int yCursor

event handler mouse Y cursor coordinates

fontHeight

int fontHeight

height font size of current font

fontLeading

int fontLeading

leading font size of current font

title

java.lang.String title

ARG: opt. from user. If drawLabel

plotStyleMode

int plotStyleMode

plot mode style: 0=line, 1=circle, 2=curve

zoomBarsMag

int zoomBarsMag

zoom magnification: by 1X, 2X, 5X, 10X, 20X mod

didDataSetupFlag

boolean didDataSetupFlag

set by setupData() if successful

drawLabelsFlag

boolean drawLabelsFlag

ARG: draw labels for larger version

drawAdditionalDataFlag

boolean drawAdditionalDataFlag

draw title & additional data if larger format.

drawIntoImageFlag

boolean drawIntoImageFlag

set if draw plot to GIF file

oGifFileName

java.lang.String oGifFileName

full Gif file path name

Class ExprProfilePanel implements Serializable

Serialized Fields

prp

ProtPlot prp

link to global prpxplorer instance

epc

ExprProfileCanvas epc

expression profile canvas we put into panel

Class ExprProfilePopup implements Serializable

Serialized Fields

prp

ProtPlot prp

link to global ProtPlot instance

eppl

ExprProfilePanel eppl

panel we put into this popup window

preferredHeight

int preferredHeight

prefered height canvas size, 0 to use defaults

preferredWidth

int preferredWidth

prefered width canvas size, 0 to use defaults

showErrBarsCheckBox

java.awt.Checkbox showErrBarsCheckBox

checkbox to show error bars

saveAsGIF

java.awt.Button saveAsGIF

Save display as GIF file

plotStyleButton

java.awt.Button plotStyleButton

plot style (line, circle, curve) button

zoomBarsButton

java.awt.Button zoomBarsButton

zoom magnification button

addButtonsFlag

boolean addButtonsFlag

flag: if false, don't add title or Close button

Class ExprProfileScrollPane implements Serializable

Serialized Fields

prp

ProtPlot prp

link to global ProtPlot instance

util

UtilPRP util

sepp

ShowExprProfilesPopup sepp

Parent window

title

java.lang.String title

title for entire EP. panel

mEPprotList

int[] mEPprotList

List of mPids being used for EP panel

nProteins

int nProteins

# genes in exprProfileCL

N_EP_PROTEINS

int N_EP_PROTEINS

sbSize

int sbSize

width of scroll bar control

nGridElements

int nGridElements

i.e. nRows*nCols

nRows

int nRows

# of rows in the Grid

nCols

int nCols

# of columns in the Grid

mNbr

int mNbr

.mList[mNbr] in database to display

nEPproteins

int nEPproteins

# genes to display in popup EP plot

epOverlayList

ExprProfile[] epOverlayList

list of overlay expr. profiles

epplList

ExprProfilePanel[] epplList

Expr Profs [nGridElements]

cTitle

java.lang.String[] cTitle

[0:nProteins-1] "#MasterProtein_ID"

nHP_E

int nHP_E

# of HPS in an Expr Profile

plotStyleMode

int plotStyleMode

plot style mode: 0=line, 1=circle, 2=curve

zoomBarsMag

int zoomBarsMag

1X, 2X, 5X, 10X pass through to EP panel

epPanel

java.awt.Panel epPanel

holds grid of ExprProfilePanel's

vs

java.awt.Scrollbar vs

vertical scroll bar

xList

float[] xList

[nProteins*nHP_E] EP overlay coords

yList

float[] yList

[nProteins*nHP_E] EP overlay coords

nPoints

int nPoints

nProteins*nHP_E

bestProtein

int bestProtein

gene if mouse event

bestSample

int bestSample

Sample if mouse event

bestMid

int bestMid

gene clone ID if mouse event

bestIntens

float bestIntens

intensity if mouse event

Class PopupDialog implements Serializable

Serialized Fields

answer

boolean answer

value returned when yes or no was clicked

Class PopupDialog.MainDialog implements Serializable

Serialized Fields

this$0

PopupDialog this$0

answer

boolean answer

answer when exit dialog

Class PopupDialogQuery implements Serializable

Serialized Fields

prp

ProtPlot prp

link to global instance to prpxplorer

data

java.lang.String data

for returning data back to prp

colSize

int colSize

# of columns to display

width

int width

size of frame

height

int height

size of frame

frame

java.awt.Frame frame

popup frame instance

textField

java.awt.TextField textField

place text to be edited here

label

java.awt.Label label

for data label

optionPanel

java.awt.Panel optionPanel

for options

optionChoice

java.awt.Choice optionChoice

opt. option choice list

addButtonsCnt

int addButtonsCnt

# of buttons to add. if 0, then none, if 1, then add CONTINUE, if 2 then add OK and CANCEL.

alertDone

boolean alertDone

button pressed flag

sleepFlag

boolean sleepFlag

wait for button to be pushed

listener

java.awt.event.ActionListener listener

Tried this instead of "this"

spaces

java.lang.String spaces

DEF_COL_SIZE spaces

optionValues

java.lang.String[] optionValues

list of option values if present

nOptions

int nOptions

optionValues[0:nOptions]

Class PopupStatusWindow implements Serializable

Serialized Fields

prp

ProtPlot prp

controlPanel

java.awt.Panel controlPanel

hideButton

java.awt.Button hideButton

hide window button

quitButton

java.awt.Button quitButton

quit the application button

txtField1

java.awt.TextField txtField1

txtField2

java.awt.TextField txtField2

txtField3

java.awt.TextField txtField3

txtField4

java.awt.TextField txtField4

Class ShowExprProfilesPopup implements Serializable

Serialized Fields

prp

ProtPlot prp

util

UtilPRP util

link to global instance

popupName

java.lang.String popupName

popupPropertyBits

int popupPropertyBits

ARG: for PopupRegistry

title

java.lang.String title

ARG: for PopupRegistry

epsp

ExprProfileScrollPane epsp

scrollable panel of ExprProfilePanel's

epPane

java.awt.ScrollPane epPane

Scrollable panel

gp

java.awt.Panel gp

Grid panel

mEPprotList

int[] mEPprotList

Master Protein List being used for EP plots

nProteins

int nProteins

# of genes in expression profile

frameWidth

int frameWidth

this frame size computed

frameHeight

int frameHeight

this frame size computed

epspStatusLabel

java.awt.Label epspStatusLabel

closeButton

java.awt.Button closeButton

plotStyleButton

java.awt.Button plotStyleButton

zoomBarsButton

java.awt.Button zoomBarsButton

plotStyleMode

int plotStyleMode

Mode for plotting points in the expr profile where: 0=(bar) line, 1=circle, 2=curve

zoomBarsMag

int zoomBarsMag

data magnification 1X, 2X, 5X, 10X, 20X

showFilteredLinesFlag

boolean showFilteredLinesFlag

Class ShowScatterPlotPopup implements Serializable

Serialized Fields

prp

ProtPlot prp

instance of ProtPlot

eh

EventHandlerPRP eh

instance of EventHandlerPRP

fil

Filter fil

Instance of Data Filter.

rpt

ReportPRP rpt

instance of ReportPRP

util

UtilPRP util

instance of UtilPRP

title

java.lang.String title

ARG: title of popup plot

panelWidth

int panelWidth

default size - must be set here!

panelHeight

int panelHeight

default size - must be set here!

mbar

java.awt.MenuBar mbar

menu bar for GUI

menuFont

java.awt.Font menuFont

Define the menu fonts

sPanel

java.awt.Panel sPanel

panel which holds scrollable canvas

pValueThrSlider

java.awt.Scrollbar pValueThrSlider

pValue threshold slider

distThrSlider

java.awt.Scrollbar distThrSlider

Cluster distance threshold slider

nbrSamplesThrSlider

java.awt.Scrollbar nbrSamplesThrSlider

Number of samples threshold slider

nbrProteinsThrSlider

java.awt.Scrollbar nbrProteinsThrSlider

Number of proteins/samples threshold slider

vertLBscr

java.awt.Scrollbar vertLBscr

vertical (top,bottom) scrollers for the for canvas

vertUBscr

java.awt.Scrollbar vertUBscr

vertical (top,bottom) scrollers for the for canvas

horizLBscr

java.awt.Scrollbar horizLBscr

Horizontal (left,right) scrollers for the for canvas

horizUBscr

java.awt.Scrollbar horizUBscr

Horizontal (left,right) scrollers for the for canvas

exprRangePanel

java.awt.Panel exprRangePanel

Panel to hold the Expr Range scrollers

expRngLBscr

java.awt.Scrollbar expRngLBscr

Expression Range vertical (top,bottom) scrollers

expRngUBscr

java.awt.Scrollbar expRngUBscr

Expression Range vertical (top,bottom) scrollers

exprUBLabel

java.awt.Label exprUBLabel

"Expression upper limit" or "Ratio upper limit"

exprLBLabel

java.awt.Label exprLBLabel

"Expression lower limit" or "Ratio lower limit"

distThrLabel

java.awt.Label distThrLabel

"Cluster distance thresh."

nbrSamplesLabel

java.awt.Label nbrSamplesLabel

"# samples threshold"

nbrProteinsLabel

java.awt.Label nbrProteinsLabel

"# proteins/sample threshold"

pValueLabel

java.awt.Label pValueLabel

"P-value threshold"

exprUBValueLabel

java.awt.Label exprUBValueLabel

"Expression upper limit" or "Ratio upper limit" value

exprLBValueLabel

java.awt.Label exprLBValueLabel

"Expression lower limit" or "Ratio lower limit" value

distThrValueLabel

java.awt.Label distThrValueLabel

"Cluster distance thresh." value

nbrSamplesValueLabel

java.awt.Label nbrSamplesValueLabel

"# samples threshold" value

nbrProteinsValueLabel

java.awt.Label nbrProteinsValueLabel

"# proteins/sample threshold"

pValueValueLabel

java.awt.Label pValueValueLabel

"P-value threshold" value

sampleChoice

java.awt.Choice sampleChoice

Choice selector for setting sample lists

statusCheckBox

java.awt.Checkbox statusCheckBox

HideStatus/ShowStatus selection

exprCheckBox

java.awt.Checkbox exprCheckBox

Expression/Location selection

filterCheckBox

java.awt.Checkbox filterCheckBox

Filter/Don't-Filter selection [DEPRICAED]

useXYsetCheckBox

java.awt.Checkbox useXYsetCheckBox

mouseOverCheckBox

java.awt.Checkbox mouseOverCheckBox

Show Mouse-over info

logMWscalingCheckBox

java.awt.Checkbox logMWscalingCheckBox

use Log MW scaling

accessGenomicDBCheckBox

java.awt.Checkbox accessGenomicDBCheckBox

access genomic DB via the Web if enabled and DB was selected

miXYmissing

java.awt.MenuItem miXYmissing

MenuItem for "Report X&Y sets statistics of proteins passing missing protein filter"

miEPmissing

java.awt.MenuItem miEPmissing

MenuItem for ""Report EP set statistics of proteins passing missing protein filter"

miClustSimilar

java.awt.MenuItem miClustSimilar

MenuItem for "Cluster similar proteins to current protein by EP profile"

miChkBoxFilterByProteinFamily

java.awt.CheckboxMenuItem miChkBoxFilterByProteinFamily

"Filter data by protein families [CB]"

miChkBoxFilterByTissue

java.awt.CheckboxMenuItem miChkBoxFilterByTissue

"Filter data by tissues [CB]"

miChkBoxFilterByExprRange

java.awt.CheckboxMenuItem miChkBoxFilterByExprRange

Filter data by expression range [CB]"

miChkBoxShowXandYsamplesMode

java.awt.CheckboxMenuItem miChkBoxShowXandYsamplesMode

"Show both X and Y samples if doing X/Y filtering [CB]"

miChkBoxAutoUpdateRptMode

java.awt.CheckboxMenuItem miChkBoxAutoUpdateRptMode

"Auto-update reports if the state changes [CB]"

miChkBoxSortAssendingRptMode

java.awt.CheckboxMenuItem miChkBoxSortAssendingRptMode

"Sort report assending order[CB]"

miPrevPlotCB

java.awt.CheckboxMenuItem miPrevPlotCB

Last Show Plot mode for use in toggling XY set checkbox

miChkBoxReqAtLeastNsamples

java.awt.CheckboxMenuItem miChkBoxReqAtLeastNsamples

"Filter by requiring at least N samples [RB]"

miChkBoxReqAtMostNsamples

java.awt.CheckboxMenuItem miChkBoxReqAtMostNsamples

"Filter by requiring at most N samples [RB]"

miChkBoxUseSavedClusterSet

java.awt.CheckboxMenuItem miChkBoxUseSavedClusterSet

"Filter by AND of Saved Clustered proteins [CB]"

miChkBoxUseSavedFilterSet

java.awt.CheckboxMenuItem miChkBoxUseSavedFilterSet

"Filter by AND of Saved Filtered proteins [CB]"

miChkBoxFilterByXYmissingProteins

java.awt.CheckboxMenuItem miChkBoxFilterByXYmissingProteins

"Filter by X & Y sets missing and > N samples [CB]"

miChkBoxFilterByXYtTest

java.awt.CheckboxMenuItem miChkBoxFilterByXYtTest

"Filter by X & Y sets t-test results [CB]"

miChkBoxFilterByXY_KStest

java.awt.CheckboxMenuItem miChkBoxFilterByXY_KStest

"Filter by X & Y sets Kolmogorov-Smirnov-test results [CB]"

miChkBoxUsePseudocolor

java.awt.CheckboxMenuItem miChkBoxUsePseudocolor

"Use pseudocolor else grayscale for expression [CB]

miChkBoxShowFilterResults

java.awt.CheckboxMenuItem miChkBoxShowFilterResults

"Show filter results [CB]"

miChkBoxLogMW

java.awt.CheckboxMenuItem miChkBoxLogMW

"Use log of (MW) [CB]"

miChkBoxMouseOver

java.awt.CheckboxMenuItem miChkBoxMouseOver

"Enable mouse-over to see data [CB]"

miChkBoxShowExpr

java.awt.CheckboxMenuItem miChkBoxShowExpr

"Show expression data else just position [CB]"

miChkBoxUseVarRadiusExpr

java.awt.CheckboxMenuItem miChkBoxUseVarRadiusExpr

"Use radius proportional to expression else constant [CB]"

miChkBoxShowClusteredProteins

java.awt.CheckboxMenuItem miChkBoxShowClusteredProteins

"Show clustered proteins by black boxes [CB]"

miChkBoxAccessGenomicDBs

java.awt.CheckboxMenuItem miChkBoxAccessGenomicDBs

"Access a genomic Web server if you click on a spot [CB]"

miChkBoxSwissProtServer

java.awt.CheckboxMenuItem miChkBoxSwissProtServer

"Use Swiss-Prot Web server [RB] "

miChkBoxPIRProClassServer

java.awt.CheckboxMenuItem miChkBoxPIRProClassServer

"Use PIR ProClass Web server [RB]"

miChkBoxGenBankServer

java.awt.CheckboxMenuItem miChkBoxGenBankServer

"Use GenBank Web server [RB]

miChkBoxClusterDistWEIGHT

java.awt.CheckboxMenuItem miChkBoxClusterDistWEIGHT

"Use weighted distance metric [RB]

miChkBoxClusterDistAVG_ALL_DATA

java.awt.CheckboxMenuItem miChkBoxClusterDistAVG_ALL_DATA

"Use average all data distance metric [RB]

miChkBoxClusterDistMAP_LOW_VALUES

java.awt.CheckboxMenuItem miChkBoxClusterDistMAP_LOW_VALUES

"Use map low values distance metric [RB]

miChkBoxUseTotPRPfiles

java.awt.CheckboxMenuItem miChkBoxUseTotPRPfiles

"Build DB from XXX_tot.prp files else from XXX_under200k.prp files"

miChkBoxUseExprDataMode

java.awt.CheckboxMenuItem miChkBoxUseExprDataMode

"Show current sample expression data [RB]"

miChkBoxUseEPsetExprDataMode

java.awt.CheckboxMenuItem miChkBoxUseEPsetExprDataMode

"Show current sample expression data [RB]"

miChkBoxUseRGratioMode

java.awt.CheckboxMenuItem miChkBoxUseRGratioMode

"Show X-samples/Y-sample ratio (Red=X + Green=Y) data [RB]"

miChkBoxUseCmapRatioMode

java.awt.CheckboxMenuItem miChkBoxUseCmapRatioMode

"Show samplesX/sampleY ratio range color map [RB]"

miChkBoxUseXYSetCmapRatioMode

java.awt.CheckboxMenuItem miChkBoxUseXYSetCmapRatioMode

"Show X-Set-samples /X-Set-samples ratio range color map [RB]"

miChkBoxDisplayXYscatterplot

java.awt.CheckboxMenuItem miChkBoxDisplayXYscatterplot

"Display (X vs Y) else (Mw vs pI) scatterplot [CB]"

miChkBoxOutsideRatioRange

java.awt.CheckboxMenuItem miChkBoxOutsideRatioRange

"Filter by (X/Y) outside of [minRatioVal:maxRatioVal] sliders"

miChkBoxUseExprPlotMode

java.awt.CheckboxMenuItem miChkBoxUseExprPlotMode

"Popup Expression Profile plots [CB]"

miChkBoxUseLocalDoc

java.awt.CheckboxMenuItem miChkBoxUseLocalDoc

"Use local documentation else ProtPlot server"

logScalingFlag

boolean logScalingFlag

toggle with Linear/Log button

titleLabel

java.awt.Label titleLabel

title for the main window

cMap

java.awt.Color[] cMap

The pseudocolor or grayscale colormap [0:255] for drawing expression data over the range of [0.0 : 1.0]. Setup in makeColormap().

eColor

java.awt.Color[] eColor

The 10 pseudocolors[0:9] for drawing non-linear expression mappings using eVap[gray] function. Setup in makeColormap().

eMap

float[] eMap

The non-linear mapping (typically exponential) from [0:255] to [0.0 : 1.0]. Setup in makeColormap() for expresion mapping.

eMapMax

float[] eMapMax

The 10 highest eMap[] values corresponding to 10 eColor[] values for expression mapping.

eCmapColor

java.awt.Color[] eCmapColor

9 color Colormap for Cmap ratio scale factor color map

eCMapRatios

float[] eCMapRatios

The 9 ratio values for Cmap ratio scale factor color map

rColor

java.awt.Color[] rColor

[TODO] The 256 pseudocolors[0:255] colors for drawing non-linear ratio mappings using rMap[gray] function where gray is the mapping of ratio (exprX,exprY) to gray. Setup in makeColormap().

rMap

float[] rMap

[TODO] The non-linear mapping (typically exponential) from [0:255] to [0.01 : 10.0]. Setup in makeColormap() for ratio mapping. We then scale this to the actual ratio range [minRatioSample : maxRatioSample].

ppns

PopupPRPlistSelector ppns

popup PRP list name selector window created when needed

pfns

PopupFamilyNameSelector pfns

Popup tissue name selector window created when needed

ptns

PopupTissueNameSelector ptns

Popup tissue name selector window created when needed

phelp

ShowStringPopup phelp

Popup help window

filterSEPP

ShowExprProfilesPopup filterSEPP

popup scrollable EP list for filtered proteins

clusterSEPP

ShowExprProfilesPopup clusterSEPP

popup scrollable EP list for clustered proteins

defGifFile

java.lang.String defGifFile

default output gif file name

dwSP

DrawProtScatterPlot dwSP

Scrollable Scatterplot canvas

pdq

PopupDialogQuery pdq

hidden popup dialog

Class ShowStringPopup implements Serializable

Serialized Fields

prp

ProtPlot prp

link to global ProtPlot instance

spp

ShowScatterPlotPopup spp

link to instance

saveAsButton

java.awt.Button saveAsButton

"SaveAs" .txt button

rptType

java.lang.String rptType

Type of report: "Help", "FilterRpt", "EPFilterRpt", "XYEPmissingRpt", "EPsamplesRpt", "StateRpt", "SampleAssignRpt", "SampleNbrsRpt", "SimClusterRpt",

title

java.lang.String title

string for title of frame

savedMsg

java.lang.String savedMsg

message after Saved Txt into file

textReport

java.lang.String textReport

copy of text in textArea

defTxtFile

java.lang.String defTxtFile

textarea

java.awt.TextArea textarea

Text area GUI for main report

viewClusterBoxesCheckBox

java.awt.Checkbox viewClusterBoxesCheckBox

toggle black boxes on clustered proteins in scatterplot

optReportMode

int optReportMode

Optional Report mode if > 0

fntSize

int fntSize

font size

nRows

int nRows

# of character rows to show

nCols

int nCols

# of character cols to show

alertOK

boolean alertOK

Flag: set true if popupName is "ALERT"

mode

int mode

mode of operation used in creating this window. Used in how we close the window