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() - Method in class ProtPlot

A

a_count - Variable in class WriteGifEncoder
accept(File, String) - Method in class ShowScatterPlotPopup: accept() - filter used to test if file should be in directory list.
accessGenomicDBCheckBox - Variable in class ShowScatterPlotPopup: access genomic DB via the Web if enabled and DB was selected
accum - Variable in class WriteGifEncoder
actionPerformed(ActionEvent) - Method in class EventHandlerPRP: actionPerformed() - Handle Control panel button clicks or menu items.
actionPerformed(ActionEvent) - Method in class ExprProfilePopup: actionPerformed() - event handler for button clicks
actionPerformed(ActionEvent) - Method in class PopupDialog.MainDialog: actionPerformed() - button press handler- close window
actionPerformed(ActionEvent) - Method in class PopupDialogQuery: actionPerformed() - Handle button clicks
actionPerformed(ActionEvent) - Method in class PopupFamilyNameSelector: actionPerformed() - Handle button clicks
actionPerformed(ActionEvent) - Method in class PopupPRPlistSelector: actionPerformed() - Handle button clicks
actionPerformed(ActionEvent) - Method in class PopupStatusWindow: actionPerformed() - Handle button clicks
actionPerformed(ActionEvent) - Method in class PopupTissueNameSelector: actionPerformed() - Handle button clicks
actionPerformed(ActionEvent) - Method in class ShowExprProfilesPopup: actionPerformed() - Handle button clicks
actionPerformed(ActionEvent) - Method in class ShowScatterPlotPopup: actionPerformed() - Handle Control panel button clicks or menu items.
actionPerformed(ActionEvent) - Method in class ShowStringPopup: actionPerformed() - Handle button clicks
addButtonsCnt - Variable in class PopupDialogQuery: # of buttons to add.
addButtonsFlag - Variable in class ExprProfilePopup: flag: if false, don't add title or Close button
addPRPfile(String, String) - Method in class GetListOfPRPs: addPRPfile() - Add prpFile to PRP database
adjustmentValueChanged(AdjustmentEvent) - Method in class EventHandlerPRP: adjustmentValueChanged() - handle scroll events.
adjustmentValueChanged(AdjustmentEvent) - Method in class ExprProfileScrollPane: adjustmentValueChanged() - handle scroll events and cause repaint.
adjustmentValueChanged(AdjustmentEvent) - Method in class ShowScatterPlotPopup: adjustmentValueChanged() - handle scroll events.
alertDone - Variable in class PopupDialogQuery: button pressed flag
alertOK - Variable in class ShowStringPopup: Flag: set true if popupName is "ALERT"
alertTimeout(String) - Method in class PopupDialogQuery: alertTimeout() - update the popup dialog msg - wait for "Continue"
allocLocalEPdataArrays(boolean) - Method in class Filter: allocLocalEPdataArrays() - setup or change EP sets array allocations used by Filter
allocLocalXYdataArrays(boolean) - Method in class Filter: allocLocalXYdataArrays() - setup or change X, Y, or EP sets array allocations used by Filter
allowClusterReportUpdatesFlag - Static variable in class Cluster: flag set if clustering is enabled for the current cluster method
allowSetsFlag - Variable in class PopupPRPlistSelector: Flag is true if may set multiple samples else enforce single sample
allowXYsetsCheckBox - Variable in class PopupPRPlistSelector: allow XY sets (else single) samples Checkbox
alog10(double) - Static method in class Draw2DprotPlot: alog10() - compute alog(x) base 10.
alog10(double) - Static method in class MathPRP: alog10() - compute alog(x) base 10.
alog2(double) - Static method in class MathPRP: alog2() - compute alog(x) base 2.
answer - Variable in class PopupDialog: value returned when yes or no was clicked
answer - Variable in class PopupDialog.MainDialog: answer when exit dialog
aText - Variable in class Draw2DprotPlot
autoUpdateFlag - Variable in class ProtPlot: if we are to auto update reports, else use Update button if available

B

b - Variable in class WriteGifEncoder
bestIntens - Variable in class ExprProfileScrollPane: intensity if mouse event
bestMid - Variable in class ExprProfileScrollPane: gene clone ID if mouse event
bestProtein - Variable in class ExprProfileScrollPane: gene if mouse event
bestSample - Variable in class ExprProfileScrollPane: Sample if mouse event
BITS - Static variable in class WriteGifEncoder
blueBits(int) - Method in class MedianCut: blueBits() - Get 8-bit blue component of a 15-bit color 8-bit pixel with low 3 bits zero.
bLUT - Variable in class MedianCut: [0:255] Blue Color map look up table
bmax - Variable in class MC_Cube
bmin - Variable in class MC_Cube
browserTitle - Variable in class ProtPlot: browser title
bubbleSortIndex(float[], int, boolean) - Static method in class UtilPRP: bubbleSortIndex() - sort copy of float[0:len-1] data with bubble sort, return index[].
bubbleSortIndex(String[], int, boolean, boolean) - Static method in class UtilPRP: bubbleSortIndex() - sort copy of String[0:len-1] data with bubble sort, return index[].
buttonFontFamily - Variable in class ProtPlot: default button font family name

C

calcBaseImage() - Method in class Draw2DprotPlot: calcBaseImage() - calculate base image for plot into img.
calcDistIJ(int, int) - Method in class Cluster: calcDistIJ() - compute the distance between midI and midJ using distMode method.
calcEPstatistics() - Method in class Filter: calcEPstatistics() - compute primary statistics for EP set data in epData[0:nEP-1].
calcFprobFromVariances(int, int, double, double) - Method in class StatisticsPRP: calcFprobFromVariances() - calculate 2-tailed f probility that variables are same.
calcHistStats(String, int, float[], int) - Method in class StatisticsPRP: calcHistStats() - compute and analyze histogram generating statistics.
calcHistStats(String, int, float[], int, int[]) - Method in class StatisticsPRP: calcHistStats() - compute and analyze a histogram for whatever range of data is given.
calcKS_DandPvalues(double[], int, double[], int) - Method in class StatisticsPRP: calcKS_DandPvalues() - calculate Kolmogorov-Smirnov ksD, pKS, dFks from (n1,data1) and (n2,data2).
calcMeanDistIJ() - Method in class Cluster: calcMeanDistIJ() - compute mean distances for all samples
calcMPID2PIDmap() - Method in class ProtPlot: calcMPID2PIDmap() - generate the mPid to pid map for all samples.
calcPearsonCorrCoef(float[], float[], int, boolean) - Static method in class MathPRP: calcPearsonCorrCoef() - compute Pearson correlation coefficient The data is data1[0:n-1] and data2[0:n-1].
calcTandPvalues(int, int, double, double, double, double) - Method in class StatisticsPRP: calcTandPvalues() - calculate f, t, p, dF from (n1,m1,s1) and (n2,m2,s2).
calcXYstat(int, float[], float[], String, String) - Static method in class MathPRP: calcXYstat() - compute correlation statistics string for display rSq=.., n=.., X(mn+-sd)=(..+-..), Y(mn+-sd)=(..+-..) This method was derived from GELLAB-II which was derived from Snedecore and Chochran Statistical Methods.
calcXYstatistics() - Method in class Filter: calcXYstatistics() - compute primary statistics for X and Y sets for current x(y)Data[].
changeStateFile(boolean) - Method in class ShowScatterPlotPopup: changeStateFile() - open up a new state startup database file.
char_init() - Method in class WriteGifEncoder: char_init() - Set up the 'byte output' routine
char_out(byte, FileOutputStream) - Method in class WriteGifEncoder: char_out() - add char to end of current packet, and if it is 254 characters, flush the packet to disk.
checkBoxPanel - Variable in class PopupFamilyNameSelector
checkBoxPanel - Variable in class PopupPRPlistSelector
checkBoxPanel - Variable in class PopupTissueNameSelector: Frame of tissue name checkboxes
checkSamplesFilter(int) - Method in class Filter: checkSamplesFilter() - check Proteins (pX,pY) to see if it passed filter.
chkDirFinalSeparator(String, String) - Static method in class UtilPRP: chkDirFinalSeparator() - make dir path end in fileSeparator.
cityBlockDist(float[], float[], int, boolean) - Static method in class MathPRP: cityBlockDist() - compute city-block distance of 2 vectors.
cl_block(FileOutputStream) - Method in class WriteGifEncoder: cl_block() - table clear for block compress Clear out the hash table.
cl_hash(int) - Method in class WriteGifEncoder: cl_hash() - reset code table
clear_flg - Variable in class WriteGifEncoder: 80% occupancy
clearAllButton - Variable in class PopupPRPlistSelector: "Clear all" window button
ClearCode - Variable in class WriteGifEncoder
clearDynamicState() - Method in class ProtPlot: clearDynamicState() - reset dynamic state variables in prp instance
close() - Method in class ShowExprProfilesPopup: close() - close this popup
close(boolean) - Method in class ShowStringPopup: close() - close this popup and reset flags if needed
closeAll(boolean) - Method in class ShowScatterPlotPopup: closeAll() - close all windows
closeButton - Variable in class PopupFamilyNameSelector: close window button
closeButton - Variable in class PopupPRPlistSelector: close window button
closeButton - Variable in class PopupTissueNameSelector: close window button
closeButton - Variable in class ShowExprProfilesPopup
clust - Variable in class ProtPlot: Instance of Cluster
CLUST_KMEANS_PROTEINS_METHOD - Static variable in class Cluster: K-means proteins clustering method
CLUST_SIMILAR_PROTEINS_METHOD - Static variable in class Cluster: Similar proteins clustering method
Cluster - class Cluster.: Class Cluster.java - Cluster the current ProtPlot data.
cluster() - Method in class Cluster: cluster() - cluster if allowClusterReportUpdatesFlag enabled using the current clusterMethod.
Cluster(ProtPlot) - Constructor for class Cluster: Cluster() - constructor to setup globals for clustering
clusterDataReadyFlag - Variable in class Cluster: flag that indicates that the cluster data exists
clusterKMeansProteins() - Method in class Cluster: clusterKMeansProteins() - cluster proteins passing the K-means filter.
clusterKMeansProteins(boolean) - Method in class Cluster: clusterKMeansProteins() - cluster proteins passing the filter similar to the current protein.
clusterMethod - Static variable in class Cluster: Cluster method computation method using the CLUST_xxxx values
clusterNameSetFile - Variable in class ProtPlot: File name of Cluster Named Protein set file if it exists
clusterNbr - Variable in class Protein: Cluster number used with K-means and other divisive clustering methods NOTE: ONLY used with Master Protein List, it is -1 otherwise.
clusterSEPP - Variable in class ShowScatterPlotPopup: popup scrollable EP list for clustered proteins
clusterSimilarProteins() - Method in class Cluster: clusterSimilarProteins() - cluster proteins passing the filter similar to the current protein.
clusterSimilarProteins(boolean) - Method in class Cluster: clusterSimilarProteins() - cluster proteins passing the filter similar to the current protein.
cMap - Variable in class ShowScatterPlotPopup: The pseudocolor or grayscale colormap [0:255] for drawing expression data over the range of [0.0 : 1.0].
cnt - Variable in class MC_Cube
codetab - Variable in class WriteGifEncoder
COG_URL - Static variable in class ProtPlot
colorMax - Variable in class MedianCut: # of non-zero bins in hist15[]
colSize - Variable in class PopupDialogQuery: # of columns to display
compress(int, FileOutputStream) - Method in class WriteGifEncoder: compress() - GIF Image compression - modified 'compress'.
CONSOLE_FLAG - Static variable in class ProtPlot: Always TRUE
controlPanel - Variable in class PopupFamilyNameSelector
controlPanel - Variable in class PopupPRPlistSelector
controlPanel - Variable in class PopupStatusWindow
controlPanel - Variable in class PopupTissueNameSelector: Frame of tissue name checkboxes
copyFile(String, String, String, int) - Method in class UtilPRP: copyFile() - binary copy of one file or URL toa local file
count - Variable in class WriteGifEncoderHashitem
createPopupPlot(String) - Method in class ShowScatterPlotPopup: createPopupPlot() - create a 2D gel popup scatterplot from raw data.
cTitle - Variable in class ExprProfileScrollPane: [0:nProteins-1] "#MasterProtein_ID"
cubeList - Variable in class MedianCut: list of cubes
cur_accum - Variable in class WriteGifEncoder
cur_bits - Variable in class WriteGifEncoder
curMPID - Variable in class ProtPlot: Current mPid for current sample proteins index.
curMProt - Variable in class ProtPlot: current Master Protein object if any
curPID - Variable in class ProtPlot: current pid protein id if any.
curProteinColor - Variable in class Draw2DprotPlot
curSample - Variable in class ProtPlot: current index of the ReadPRP PRP database
curSampleNameFile - Variable in class ProtPlot: Name of the current sample Name File
cvd2s(double, int) - Static method in class UtilPRP: cvd2s() - convert double to string with precision # of digits If precision > 0 then limit # of digits in fraction
cvEPdata - Variable in class Filter: computed Coefficient of variation all EP set data for current protein
cvExpr - Variable in class ExprProfile: CV (stdDevExpr/meanExpr) of expression of the sampleData[] values.
cvf2s(float, int) - Static method in class UtilPRP: cvf2s() - convert float to string with precision # of digits If precision > 0 then limit # of digits in fraction
cvNonLinearScroller2StateValue(float, float, float, int) - Method in class ShowScatterPlotPopup: cvNonLinearScroller2StateValue() - convert non-linear Scrollbar value to a State value:
cvNonLinearState2ScrollerValue(float, float, float, int) - Method in class ShowScatterPlotPopup: cvNonLinearState2ScrollerValue() - convert non-linear State value to a Scroller value:
cvPrecision - Variable in class Draw2DprotPlot
cvs2d(String) - Static method in class UtilPRP: cvs2d() - convert String to double
cvs2f(String) - Static method in class UtilPRP: cvs2f() - convert String to float
cvs2f(String, float) - Static method in class UtilPRP: cvs2f() - convert String to float
cvs2i(String) - Static method in class UtilPRP: cvs2i() - convert String to int
cvs2i(String, int) - Static method in class UtilPRP: cvs2i() - convert String to int
cvs2long(String) - Static method in class UtilPRP: cvs2long() - convert String to int
cvtFamiliesStr(long) - Method in class ReadFamilies: cvtFamiliesStr() - lookup family strings for familyBits
cvtFamilyNamesToBits(String) - Method in class ReadFamilies: cvtFamilyNamesToBits() - convert a String list of family names to familyBits.
cvtImg24toImg8(int) - Method in class MedianCut: cvtImg24toImg8() - Uses Heckbert's median-cut algorithm to divide the color space defined by "hist15[]" into "maxcubes" cubes.
cvtSpacesToUnderscores(String) - Static method in class UtilPRP: cvtSpacesToUnderscores() - replace spaces and other illegal file name characters with '_' chars to make file names highly portable.
cvtTissueNamesToBits(String) - Method in class ReadTissues: cvtTissueNamesToBits() - convert tissue names to tissueBits Eg.
cvtTissuesStr(long) - Method in class ReadTissues: cvtTissuesStr() - lookup tissues from the tissueBits
cvtUnderscores2Spaces(String) - Static method in class UtilPRP: cvtUnderscores2Spaces() - change underscores to spaces
cvtValueToStars(float, float, int, boolean) - Static method in class UtilPRP: cvtValueToStars() - cvt val in[0:valMax] to "****"+" " string where the maximum # of stars for v==vMax is specified.
cvXdata - Variable in class Filter: computed Coefficient of variation all X set data for current protein
cvYdata - Variable in class Filter: computed Coefficient of variation all Y set data for current protein

D

data - Variable in class PopupDialogQuery: for returning data back to prp
dataFile - Variable in class ReadPRP: full name of data file to use
dateStr() - Static method in class UtilPRP: dateStr() - return a new Date string of the current day and time
DBUG_6_SAMPLES - Static variable in class ProtPlot: DBUG max # of 6 samples to test multiple samples
DBUG_LOCALHOST_HOMEPAGE - Static variable in class ProtPlot: Debug Update commands using LOCALHOST_HOMEPAGE_URL
dbugCnt - Static variable in class Draw2DprotPlot: debugging counter
DEBUG - Static variable in class ProtPlot: general purpose debugging
DEBUG_MENU_CMDS - Static variable in class ProtPlot: DEBUG_MENU_CMDS value set to enable new commands being debugged 0 to enable command, -1 to disable it, -2 to not show them in the menu.
DEF_COL_SIZE - Static variable in class PopupDialogQuery: default # of columns
DEF_CUR_SAMPLE_PRP_FILE - Static variable in class ProtPlot: Default .prp startup file if none specified
DEF_SAMPLEX_PRP_FILE - Static variable in class ProtPlot: Default sample X .prp file if none specified
DEF_SAMPLEY_PRP_FILE - Static variable in class ProtPlot: Default sample Y .prp file if none specified
defaultFloat - Static variable in class UtilPRP: Default value of float for cvs2f() calls
defaultInt - Static variable in class UtilPRP: Default value of int for cvs2i() calls
defFamilies - Variable in class ReadFamilies: default list of protein families
defGifFile - Variable in class ShowScatterPlotPopup: default output gif file name
defTissues - Variable in class ReadTissues: Default list of tissues
defTxtFile - Variable in class ShowStringPopup
deleteLocalFile(String) - Method in class UtilPRP: deleteLocalFile() - delete local file.
deltaBinH - Variable in class StatisticsPRP: width of the bins computed as: nBinsH/(maxDataH-minDataH)
dF - Variable in class StatisticsPRP: CALC: degrees of freedom T or F test
dFks - Variable in class StatisticsPRP: CALC: degrees of freedom KS-test
dialogQuery(String, float) - Method in class PopupDialogQuery: dialogQuery() - query float variable
dialogQuery(String, int) - Method in class PopupDialogQuery: dialogQuery() - query int variable
dialogQuery(String, String) - Method in class PopupDialogQuery: dialogQuery() - query String variable requested
dialogQuery(String, String, String[], int) - Method in class PopupDialogQuery: dialogQuery() - query String variable int requested
didDataSetupFlag - Variable in class ExprProfile: flag: set by setupData() if successful
didDataSetupFlag - Variable in class ExprProfileCanvas: set by setupData() if successful
didDataSetupFlag - Variable in class Filter: flag: set by setupData() if successful
didStatisticsFlag - Variable in class Filter: flag: set by calcPrimaryStatisticss() if successful
disableQuitButton() - Method in class PopupStatusWindow: disableQuitButton() - after system comes up
displayURL(String) - Method in class UtilPRP: displayURL() - Display a file in the system browser.
displayXYscatterplotFlag - Variable in class ProtPlot: "Display (X vs Y) else (Mw vs pI) scatterplot [CB]"
DIST_AVG_ALL_DATA - Static variable in class Cluster: Jain method 4 for computing distance using missing values using average of all data in the database.
DIST_FISHER_LOW_VALUES - Static variable in class Cluster: method for computing distance using the Fisher clustering low values distance metric that maps low or missing values counts to a low value (i.e.
DIST_WEIGHT - Static variable in class Cluster: Jain method 3 for computing distance using missing values by weighting
distFisherLowValues(int, int) - Method in class Cluster: distFisherLowValues() - compute the Fisher clustering low values distance metric by mapping low or missing values counts to a low value (i.e.
distIJ - Variable in class Cluster: current distance between mPidI and mPidJ
distMissing(int, int) - Method in class Cluster: distMissing() - return average missing distance between mPidI and mPidJ.
distMissingIJ(int, int, int) - Method in class Cluster: distMissingIJ() - compute sample s distance between Esi and Esj for mPidI and mPidJ.
distMissingMean(int, int) - Method in class Cluster: distMissingMean() - return average missing distance between mPidI and mPidJ.
distMissingMeanIJ(int, int, int) - Method in class Cluster: distMissingMeanIJ() - compute sample s distance between Esi and Esj for mPidI and mPidJ.
distMode - Static variable in class Cluster: distance computation method using the DIST_xxxx values
distMode - Variable in class ProtPlot: distance computation method using the DIST_xxxx values
distSimilarCluster - Variable in class Cluster: distances [0:mMasterPid-1] sorted by prp.mPidSimilarCluster[] list
distThreshold - Static variable in class Cluster: Distance threshold for similarity clustering
distThreshold - Variable in class ProtPlot: Distance threshold for similarity clustering
distThrLabel - Variable in class ShowScatterPlotPopup: "Cluster distance thresh."
distThrSlider - Variable in class ShowScatterPlotPopup: Cluster distance threshold slider
distThrValUB - Variable in class ProtPlot: (Distance Threshold) Vertical slider initial value Upper Bound
distThrValueLabel - Variable in class ShowScatterPlotPopup: "Cluster distance thresh." value
dKS - Static variable in class MathPRP: RTN: K-S statistic
dMean - Variable in class Cluster: mean distances for all samples [0:nPRPs-1]
docCodeBase - Variable in class ProtPlot: Where the Reference Manual is kept
doingXYscatterPlotFlag - Variable in class Filter: set if doing display X vs Y in ratio mode
DRAW_BOX - Static variable in class ProtPlot: Plotting type: box
DRAW_CIRCLE - Static variable in class ProtPlot: Plotting type: circle
draw_MWvsPI_scatterPlot() - Method in class DrawProtScatterPlot: draw_MWvsPI_scatterPlot() - draw (Mw vs pI) scatterplot (repeatedly) of Filter data.
DRAW_PLUS - Static variable in class ProtPlot: Plotting type: plus
draw_XvsY_scatterPlot() - Method in class DrawProtScatterPlot: draw_XvsY_scatterPlot() - draw (X vs Y) scatterplot (repeatedly) of Filter data.
draw2Dplot(Graphics) - Method in class Draw2DprotPlot: draw2Dplot() - draw a plot in the current graphics context This is the main plot drawing method generally called by paint().
Draw2DprotPlot - class Draw2DprotPlot.: Class Draw2DPlot.java - draw 2D graphics protein scatterplot.
Draw2DprotPlot(ProtPlot, ShowScatterPlotPopup, String) - Constructor for class Draw2DprotPlot: Draw2Dplot() - constructor
drawAdditionalDataFlag - Variable in class ExprProfileCanvas: draw title & additional data if larger format.
drawCircle(Graphics, int, int, int, Color) - Method in class Draw2DprotPlot: drawCircle() - draw a circle The color is optional and if null it draws it in green (blue).
drawCmapRatioScaleMap(Graphics, int, int, float, float) - Method in class Draw2DprotPlot: drawCmapRatioScaleMap() - draw Cmap ratio scale factor color map on the right side of the canvas.
drawFilledColoredCircle(Graphics, int, int, int, Color) - Method in class Draw2DprotPlot: drawFilledColoredCircle() - draw filled circle of specified RGB color
drawFilledColoredCircle(Graphics, int, int, int, int, int, int) - Method in class Draw2DprotPlot: drawFilledColoredCircle() - draw filled circle of specified RGB color
drawFilledGrayCircle(Graphics, int, int, int, int) - Method in class Draw2DprotPlot: drawFilledGrayCircle() - draw filled circle of specified gray value
drawFilterStatusText(Graphics) - Method in class Draw2DprotPlot: drawFilterStatusText() - draw additional text on Filter status if required
drawGifFile(String) - Method in class Draw2DprotPlot: drawGifFile() - draw clustergram into Gif image file.
drawGifFile(String) - Method in class ExprProfileCanvas: drawGifFile() - draw expression plot into Gif image file.
drawIntoImageFlag - Variable in class Draw2DprotPlot: set if draw clustergram to GIF file
drawIntoImageFlag - Variable in class ExprProfileCanvas: set if draw plot to GIF file
drawLabelsFlag - Variable in class ExprProfileCanvas: ARG: draw labels for larger version
drawPlus(Graphics, int, int, Color) - Method in class Draw2DprotPlot: drawPlus() - draw plus sign
drawProtein(Graphics, int, int) - Method in class Draw2DprotPlot: drawProteinSpot() - draw protein mPid if passes the data filter
DrawProtScatterPlot - class DrawProtScatterPlot.: Class DrawProtScatterPlot.java - draw scatterplot using Draw2Dplot base class.
DrawProtScatterPlot(ProtPlot, ShowScatterPlotPopup) - Constructor for class DrawProtScatterPlot: DrawProtScatterPlot() - constructor
drawRedPlusGreenRatioScaleMap(Graphics, int, int, float, float) - Method in class Draw2DprotPlot: drawRedPlusGreenRatioScaleMap() - draw (Red+Green)=(X+Y) scale factor color map on right side of the canvas
drawScaleMap(Graphics, int, int, float, float) - Method in class Draw2DprotPlot: drawScaleMap() - draw scale factor color map on right side of the canvas
drawScatterPlot() - Method in class DrawProtScatterPlot: drawScatterPlot() - draw scatterplot (repeatedly) of Filter data This generates the data lists that are passed to the drawing engine.
drawScatterPlotScaleAndLabels(Graphics) - Method in class Draw2DprotPlot: drawScatterPlotScaleAndLabels() - draw scatterplot scale lines and labels
drawSquare(Graphics, int, int, int, Color) - Method in class Draw2DprotPlot: drawSquare() - draw a square The color is optional and if null it draws it in green (blue).
dupsInXYsetsFlag - Variable in class ProtPlot: flag set if there are samples that are in both the X and Y sample sets when call recalcSampleIdxLists().
dwSP - Variable in class Filter: instance of DrawProtScatterPlot
dwSP - Variable in class ShowScatterPlotPopup: Scrollable Scatterplot canvas

E

eCmapColor - Variable in class ShowScatterPlotPopup: 9 color Colormap for Cmap ratio scale factor color map
eCMapRatios - Variable in class ShowScatterPlotPopup: The 9 ratio values for Cmap ratio scale factor color map
eColor - Variable in class ShowScatterPlotPopup: The 10 pseudocolors[0:9] for drawing non-linear expression mappings using eVap[gray] function.
eDiff - Variable in class Draw2DprotPlot
eDiffBest - Variable in class Draw2DprotPlot
eh - Variable in class ProtPlot: instance of EventHandlerPRP
eh - Variable in class ShowScatterPlotPopup: instance of EventHandlerPRP
eMap - Variable in class ShowScatterPlotPopup: The non-linear mapping (typically exponential) from [0:255] to [0.0 : 1.0].
eMapMax - Variable in class ShowScatterPlotPopup: The 10 highest eMap[] values corresponding to 10 eColor[] values for expression mapping.
EOF - Static variable in class WriteGifEncoder
EOFCode - Variable in class WriteGifEncoder
ep - Variable in class ExprProfileCanvas: expression profile for mPid
EP_BUTTON_HEIGHT - Static variable in class ExprProfilePopup: hight of expression profile ploit
epc - Variable in class ExprProfilePanel: expression profile canvas we put into panel
epData - Variable in class Filter: quant data for all EP (set) members
epOverlayList - Variable in class ExprProfileScrollPane: list of overlay expr.
epp - Variable in class ProtPlot: popup expression profile window if enabled
epPane - Variable in class ShowExprProfilesPopup: Scrollable panel
epPanel - Variable in class ExprProfileScrollPane: holds grid of ExprProfilePanel's
eppl - Variable in class ExprProfilePopup: panel we put into this popup window
epplList - Variable in class ExprProfileScrollPane: Expr Profs [nGridElements]
epsp - Variable in class ShowExprProfilesPopup: scrollable panel of ExprProfilePanel's
epspStatusLabel - Variable in class ShowExprProfilesPopup
estExpr - Variable in class Protein: Normalized EST expression from CGAP/UniGene library expression value
euclidDist(float[], float[], int, boolean) - Static method in class MathPRP: euclidDist() - compute Euclidean distance or (sum dist**2) The data is data1[0:n-1] and data2[0:n-1].
EventHandlerPRP - class EventHandlerPRP.: Class EventHandlerPRP.java - implements the event handlers for ShowScatterPlotPopup.
EventHandlerPRP(ProtPlot) - Constructor for class EventHandlerPRP: EventHandlerPRP() - constructor
exprCheckBox - Variable in class ShowScatterPlotPopup: Expression/Location selection
exprLBLabel - Variable in class ShowScatterPlotPopup: "Expression lower limit" or "Ratio lower limit"
exprLBValueLabel - Variable in class ShowScatterPlotPopup: "Expression lower limit" or "Ratio lower limit" value
expRngLBscr - Variable in class ShowScatterPlotPopup: Expression Range vertical (top,bottom) scrollers
expRngUBscr - Variable in class ShowScatterPlotPopup: Expression Range vertical (top,bottom) scrollers
ExprProfile - class ExprProfile.: The class creates an nEPsamples sample expression profile object for a gene.
ExprProfile(ProtPlot, int, boolean) - Constructor for class ExprProfile: ExprProfile() - Constructor to create expresion profile object
exprProfileBits - Variable in class ExprProfile: selected expression list bits of selected samples
exprProfileBits - Variable in class ProtPlot: selected current expression list bits of selected samples
ExprProfileCanvas - class ExprProfileCanvas.: The ExprProfileCanvas is used to draw the expression profile.
ExprProfileCanvas(ProtPlot, int, String, Font, int, int, boolean) - Constructor for class ExprProfileCanvas: ExprProfileCanvas() - Constructor to display an expression profile in a canvas.
ExprProfilePanel - class ExprProfilePanel.: This class creates and displays a window containing an ExprProfileCanvas.
ExprProfilePanel(ProtPlot, int, String, Font, int, int, boolean) - Constructor for class ExprProfilePanel: ExprProfilePanel() - Constructor to display expression profile in canvas.
ExprProfilePopup - class ExprProfilePopup.: This class creates and displays a popup window containing an ExprProfilePanel.
ExprProfilePopup(ProtPlot, int, String, Font, int, int, boolean) - Constructor for class ExprProfilePopup: ExprProfilePopup() - Constructor to popup expression profile window.
ExprProfileScrollPane - class ExprProfileScrollPane.: This creates and displays a scrollable pane list of individual expression profile graphic plots.
ExprProfileScrollPane(ProtPlot, ShowExprProfilesPopup, String, int[], int, int) - Constructor for class ExprProfileScrollPane: ExprProfileScrollPane() - Create a popup grid of ExprProfile plots.
exprRangePanel - Variable in class ShowScatterPlotPopup: Panel to hold the Expr Range scrollers
exprUBLabel - Variable in class ShowScatterPlotPopup: "Expression upper limit" or "Ratio upper limit"
exprUBValueLabel - Variable in class ShowScatterPlotPopup: "Expression upper limit" or "Ratio upper limit" value
expValLB - Variable in class ProtPlot: (Expression-ratio) Vertical slider Expression initial value Lower Bound
expValUB - Variable in class ProtPlot: (Expression-ratio) Vertical slider Expression initial value Lower Bound

F

f - Variable in class StatisticsPRP: CALC: calculated f statistic
FAMILY_NAMES_FILE - Static variable in class ProtPlot: Name of file with tab-delim list of protein families (name, bits)
familyANDCheckBox - Variable in class PopupFamilyNameSelector: select BOTH family and Checkbox
familyBits - Variable in class PopupFamilyNameSelector: list of family bits
familyBits - Variable in class Protein: bits corresponding to familyList[] names
familyBits - Variable in class ReadFamilies: list of tissue family BITS [0:nFamilies-1] return all tokens/row the familyBit[i] = 2**familyNbr[i].
familyNameCheckbox - Variable in class PopupFamilyNameSelector: [0:nFamilies-1] checkboxes
familyNameFrame - Variable in class PopupFamilyNameSelector: Frame of Family name checkboxes
familyNames - Variable in class PopupFamilyNameSelector: list of family names
familyNames - Variable in class ReadFamilies: list of tissue family names [0:nFamilies-1] return all tokens/row
familyNamesFile - Variable in class ProtPlot: protein family name file
familyNamesFile - Variable in class ReadFamilies: Name of the family data tab-delimited file.
familyNbrs - Variable in class ReadFamilies: list of tissue family Numbers [0:nFamilies-1] return all tokens/row
field - Variable in class ReadPRP: fields [0:nFields]
fil - Variable in class Draw2DprotPlot: instance of Filter
fil - Variable in class EventHandlerPRP: Instance of Data Filter.
fil - Variable in class ProtPlot: Instance of Data Filter.
fil - Variable in class ReportPRP: Instance of Data Filter.
fil - Variable in class ShowScatterPlotPopup: Instance of Data Filter.
FileIOPRP - class FileIOPRP.: Class FileIOPRP.java - used to read file I/O from local disk or URL CGI server.
FileIOPRP(ProtPlot) - Constructor for class FileIOPRP: FileIOPRP() - constructor
fileSeparator - Static variable in class ProtPlot: paths, "/" or "|", or ":", depends on OS.
Filter - class Filter.: Class Filter.java - Filter the current ProtPlot data.
Filter(ProtPlot) - Constructor for class Filter: Filter() - constructor
filterCheckBox - Variable in class ShowScatterPlotPopup: Filter/Don't-Filter selection [DEPRICAED]
filterNameSetFile - Variable in class ProtPlot: File name of Filter Named Protein set file if it exists
filterSEPP - Variable in class ShowScatterPlotPopup: popup scrollable EP list for filtered proteins
fio - Variable in class ProtPlot: Instance of major classes for global data access.
flush_char(FileOutputStream) - Method in class WriteGifEncoder: flush_char() - flush packet to disk, and reset the accumulator
fntSize - Variable in class ShowStringPopup: font size
fontHeight - Variable in class ExprProfileCanvas: height font size of current font
fontLeading - Variable in class ExprProfileCanvas: leading font size of current font
frame - Variable in class PopupDialogQuery: popup frame instance
FRAME_HEIGHT - Static variable in class ProtPlot: Frame height
FRAME_WIDTH - Static variable in class ProtPlot: Frame width
frameHeight - Variable in class ShowExprProfilesPopup: this frame size computed
frameWidth - Variable in class ShowExprProfilesPopup: this frame size computed
free_ent - Variable in class WriteGifEncoder
fStat - Variable in class StatisticsPRP: CALC: f-statistic

G

g - Variable in class WriteGifEncoder
g_init_bits - Variable in class WriteGifEncoder
gammln_cof - Static variable in class MathPRP
GENBANK_BASEURL - Static variable in class ProtPlot
genBankID - Variable in class Protein: GenBank ID
genBankServerBase - Variable in class ProtPlot: GenBank server
getArrayOfTabDelimTokens(char[], int, String[]) - Method in class ReadPRP: getArrayOfTabDelimTokens() - get array of tab-delim tokens The number of expected columns is specified and if there is no more data, it will leave those cells null.
getExtraFilterData(int) - Method in class Filter: getExtraFilterData() - get extra Filter data from t-Test, KS-test etc.
getFilesInDir(String, String) - Method in class FileIOPRP: getFilesInDir() - get list of files in directory with specified file extension
getFloatValFromLine(String, StringTokenizer) - Method in class UtilPRP: getFloatValFromLine() - get next line and parse value for key 'name='.
getHelpBaseURL() - Method in class UtilPRP: getHelpBaseURL() - get the base URL for HELP based on prp.useLocalDocFlag It will either be the ProtPlot server or the /Doc/ directory
getIntValFromLine(String, StringTokenizer) - Method in class UtilPRP: getIntValFromLine() - get next line and parse value for key 'name='.
GetListOfPRPs - class GetListOfPRPs.: Class GetListOfPRPs.java - read list of PRP files and create arrays of PRP file names and PRP names without the '.prp' and map '_' to ' '.
GetListOfPRPs(ProtPlot, String, String) - Constructor for class GetListOfPRPs: GetListOfPRPs() - constructor
GetListOfPRPsFile(String) - Method in class GetListOfPRPs: GetListOfPRPsFile() - read list of PRP files into data structure If prpEndsWith is not null then build DB from files ending in prpEndsWith, else build it from files ending in ".prp".
getLongValFromLine(String, StringTokenizer) - Method in class UtilPRP: getLongValFromLine() - get next line and parse value for key 'name='.
getMinimumSize() - Method in class Draw2DprotPlot: getMinimumSize() - get the preferred size
getMinimumSize() - Method in class ExprProfileCanvas: getMinimumSize() - get the minimum preferred size
getMinimumSize() - Method in class ExprProfilePanel: getMinimumSize() - get the minimumpreferred size
getMinimumSize() - Method in class ExprProfilePopup: getMinimumSize() - get the minimum preferred window size and add on room for the buttons at the bottom.
getNextInt(StringTokenizer) - Method in class UtilPRP: getNextInt() - parse next int from StringTokenizer the integers are separated by ',' or '\n'.
getNextStrNameValFromLine(StringTokenizer) - Method in class UtilPRP: getNextStrNameValFromLine() - get next line and parse 'name=value\n'.
getPreferredSize() - Method in class Draw2DprotPlot: getPreferredSize() - get the preferred size
getPreferredSize() - Method in class ExprProfileCanvas: getPreferredSize() - get the preferred size
getPreferredSize() - Method in class ExprProfilePanel: getPreferredSize() - get the preferred size
getPreferredSize() - Method in class ExprProfilePopup: getPreferredSize() - get the preferred size
getPreferredSize() - Method in class ShowExprProfilesPopup: getPreferredSize() - get the preferred size
getPRPindexByFileName(String) - Method in class ProtPlot: getPRPindexByFileName() - lookup the PRP index by file name
getPRPindexByName(String) - Method in class ProtPlot: getPRPindexByName() - lookup the PRP index by file name
getSampleListBySubstring(String) - Method in class Filter: getSampleListBySubstring() - return a list of sample names by substring matching
getSamplesSubtitle() - Method in class ReportPRP: getSamplesSubtitle() - of samples based on plot mode
getStateStr() - Method in class UtilPRP: getStateStr() - generate a tab-delim ProtPlot State string The format is tab-delimted (name \t value \n) with one entry/line.
getStateValue(String, boolean) - Method in class ProtPlot: getStateValue() - get boolean PARAM and use default if not found.
getStateValue(String, float) - Method in class ProtPlot: getStateValue() - get float PARAM and use default if not found.
getStateValue(String, int) - Method in class ProtPlot: getStateValue() - get int PARAM and use default if not found.
getStateValue(String, long) - Method in class ProtPlot: getStateValue() - get float PARAM and use default if not found.
getStateValue(String, String) - Method in class ProtPlot: getStateValue() - get PARAM and use default if not found.
getStrValFromLine(String) - Method in class UtilPRP: getStrValFromLine() - parse value for key 'name=value\n'.
getStrValFromLine(String, StringTokenizer) - Method in class UtilPRP: getStrValFromLine() - get line and parse value for key 'name=value\n'.
GIFEncode(FileOutputStream, int, int, boolean, byte, int, int, byte[], byte[], byte[]) - Method in class WriteGifEncoder: GIFEncode() - encode the image Adapted from ppmtogif, which is based on GIFENCOD by David Rowley .
GIFNextPixel() - Method in class WriteGifEncoder: GIFNextPixel() - Return the next pixel from the image
glp - Variable in class ProtPlot: Get a list of .prp file names
gLUT - Variable in class MedianCut: [0:255] Green Color map look up table
gmax - Variable in class MC_Cube
gmin - Variable in class MC_Cube
gp - Variable in class ShowExprProfilesPopup: Grid panel
greenBits(int) - Method in class MedianCut: greenBits() - Get 8-bit green component of a 15-bit color 8-bit pixel with low 3 bits zero.

H

hashMPIDs - Variable in class ProtPlot: Hash table of Master Proteins for proteins from all PRP databases
height - Variable in class PopupDialogQuery: size of frame
height - Variable in class WriteGifEncoder
height - Variable in class MedianCut: width size of image
Height - Variable in class WriteGifEncoder
hideButton - Variable in class PopupStatusWindow: hide window button
hist - Variable in class StatisticsPRP: histogram of size [0:nBinsH-1]
hist15 - Variable in class MedianCut: [0:32K] 15-bit RGB hist.
histPtr - Variable in class MedianCut: [0:colorMax-1] points to colors in "hist15[]"
HOMEPAGE_URL - Static variable in class ProtPlot: Home page for ProtPlot
horizCaption - Variable in class Draw2DprotPlot
horizLBscr - Variable in class ShowScatterPlotPopup: Horizontal (left,right) scrollers for the for canvas
horizUBscr - Variable in class ShowScatterPlotPopup: Horizontal (left,right) scrollers for the for canvas
hsize - Variable in class WriteGifEncoder
HSIZE - Static variable in class WriteGifEncoder
HSIZE - Static variable in class MedianCut: max size of image histogram
hsValLB - Variable in class ProtPlot: (MW) Horizontal slider initial value Lower Bound
hsValUB - Variable in class ProtPlot: (MW) Horizontal slider initial value Upper Bound
htab - Variable in class WriteGifEncoder

I

iBest - Variable in class Draw2DprotPlot: Best index of spot closest to where clicked with mouse
iCurMPid - Variable in class Draw2DprotPlot
id - Variable in class MC_Cube
idx_estExpr - Variable in class ReadPRP: index for field name max EST expression
idx_FamilyName - Variable in class ReadPRP: index for field name Family Name
idx_GenBankID - Variable in class ReadPRP: index for field name GenBank ID
idx_MW - Variable in class ReadPRP: index for field name MW
idx_pI - Variable in class ReadPRP: index for field name pI
idx_SwissProtAcc - Variable in class ReadPRP: index for field name SwissProt Acc
idx_SwissProtId - Variable in class ReadPRP: index for field name SwissProt ID
idx_TissueName - Variable in class ReadPRP: index for field name Tissue Name
idxSampleEPlist - Variable in class ProtPlot: list of indices of samples used in the sampleEPlist[0:nSampleEPlist-1]
idxSampleXlist - Variable in class ProtPlot: list of indices of samples used in the X set [0:nSampleXlist-1]
idxSampleYlist - Variable in class ProtPlot: list of indices of samples used in the Y set [0:nSampleYlist-1]
idxSortALL - Variable in class PopupFamilyNameSelector: index of "ALL" in sortedNamesIdx[] list
idxSortALL - Variable in class PopupTissueNameSelector: index of "ALL" in sortedNamesIdx[] list
iHeight - Variable in class Draw2DprotPlot
img - Variable in class Draw2DprotPlot: [TODO] buffered spot image.
img - Variable in class WriteGifEncoder: Image if specified
index - Variable in class WriteGifEncoderHashitem
info1 - Variable in class Draw2DprotPlot
info2 - Variable in class Draw2DprotPlot
info3 - Variable in class Draw2DprotPlot
info4 - Variable in class Draw2DprotPlot
info5 - Variable in class Draw2DprotPlot
info6 - Variable in class Draw2DprotPlot
init() - Method in class ProtPlot: init() - allocate,clear state, read PARAMs, build GUI and start things off.
interlace - Variable in class WriteGifEncoder: 80% occupancy
Interlace - Variable in class WriteGifEncoder: 80% occupancy
isNameInList(String[], String) - Static method in class UtilPRP: isNameInList() - test if String s is in a list of strings sList[].
isSampleInExprProfileList(int) - Method in class Cluster: isSampleInExprProfileList() - test if sample s is in current Expr Profile list of samples
isTransparent - Variable in class WriteGifEncoderHashitem
isWinPCflag - Variable in class ProtPlot: set to TRUE if any Windows PC
itemStateChanged(ItemEvent) - Method in class EventHandlerPRP: itemStateChanged() - handle item state changed events NOTE: need to implement radio groups here since AWT only implements radio groups for Checkboxes, and CheckboxMenuItems.
itemStateChanged(ItemEvent) - Method in class ExprProfilePopup
itemStateChanged(ItemEvent) - Method in class PopupDialogQuery: itemStateChanged() - event handler for Choices
itemStateChanged(ItemEvent) - Method in class PopupFamilyNameSelector: itemStateChanged() - handle item state checkbox selectors.
itemStateChanged(ItemEvent) - Method in class PopupPRPlistSelector: itemStateChanged() - handle item state checkbox selectors.
itemStateChanged(ItemEvent) - Method in class PopupTissueNameSelector: itemStateChanged() - handle item state checkbox selectors.
itemStateChanged(ItemEvent) - Method in class ShowExprProfilesPopup
itemStateChanged(ItemEvent) - Method in class ShowScatterPlotPopup: itemStateChanged() - handle item state changed events NOTE: need to implement radio groups here since AWT only implements radio groups for Checkboxes, and CheckboxMenuItems.
itemStateChanged(ItemEvent) - Method in class ShowStringPopup: itemStateChanged() - handle item state changed events NOTE: need to implement radio groups here since AWT only implements radio groups for Checkboxes, and CheckboxMenuItems.
iWidth - Variable in class Draw2DprotPlot

K

ksD - Variable in class StatisticsPRP: CALC: Kolmogorov-Smirnov D statistic

L

label - Variable in class PopupDialogQuery: for data label
lastBG1 - Variable in class UtilPRP: last foreground, background colors cached
lastBG2 - Variable in class UtilPRP: last foreground, background colors cached
lastBG3 - Variable in class UtilPRP: last foreground, background colors cached
lastBG4 - Variable in class UtilPRP: last foreground, background colors cached
lastFG1 - Variable in class UtilPRP: last foreground, background colors cached
lastFG2 - Variable in class UtilPRP: last foreground, background colors cached
lastFG3 - Variable in class UtilPRP: last foreground, background colors cached
lastFG4 - Variable in class UtilPRP: last foreground, background colors cached
lblFont - Static variable in class ExprProfileCanvas
leftTextX - Variable in class Draw2DprotPlot
listener - Variable in class PopupDialogQuery: Tried this instead of "this"
ln10 - Static variable in class Draw2DprotPlot: log(x)= ln10*ln(x)
ln10 - Static variable in class MathPRP: log(10 base e
ln2 - Static variable in class MathPRP: log(2) base e
LOCALHOST_HOMEPAGE_URL - Static variable in class ProtPlot: local site Home page for ProtPlot
log10(double) - Static method in class Draw2DprotPlot: log10() - compute log(x) base 10.
log10(double) - Static method in class MathPRP: log10() - compute log(x) base 10.
log10e - Static variable in class Draw2DprotPlot: ln(x)= log10e*log(x)
log10e - Static variable in class MathPRP: log(e) base 10
log2(double) - Static method in class MathPRP: log2() - compute log(x) base 2.
log2e - Static variable in class MathPRP: log(e) base 2
log2Zero(double) - Static method in class MathPRP: log2Zero() - compute log2((x==0.0 ? 0.0 : x) - avoid log2(0.0)! This defaults log2(0.0) to log2(1.0).
logMWscalingCheckBox - Variable in class ShowScatterPlotPopup: use Log MW scaling
logMWscalingFlag - Variable in class ProtPlot: scale MW by log
logScaleX - Variable in class Draw2DprotPlot
logScaleY - Variable in class Draw2DprotPlot
logScalingFlag - Variable in class Draw2DprotPlot: Linear(false)/Log(true)
logScalingFlag - Variable in class ShowScatterPlotPopup: toggle with Linear/Log button
logZero(double) - Static method in class Draw2DprotPlot: logZero() - compute log10((x==0.0 ? 0.0 : x) - avoid log(0.0)! This defaults log10(0.0) to log(1.0).
logZero(double) - Static method in class MathPRP: logZero() - compute log10((x==0.0 ? 0.0 : x) - avoid log(0.0)! This defaults log10(0.0) to log(1.0).
lookupPIDfromMPID(int) - Method in class ReadPRP: lookupPIDfromMPID() - lookup the pid given the mPid
low - Variable in class MC_Cube
lowerTitle1 - Variable in class Draw2DprotPlot
lowerTitle2 - Variable in class Draw2DprotPlot
lvl - Variable in class MC_Cube

M

main(String[]) - Static method in class ProtPlot: main() - for ProtPlot started by standalone application.
make8BitImage() - Method in class MedianCut: make8BitImage() - Generate 8-bit image from interla 15-bit image.
makeChkBoxMenuItem(Menu, String, String, int, boolean) - Method in class ShowScatterPlotPopup: makeChkBoxMenuItem() - make CheckboxMenuItem entry in popup menu list.
makeColorMap() - Method in class EventHandlerPRP: makeColorMap() - make 255 gray value colors or if pseudocolor mode, then color range
makeColorMap() - Method in class ShowScatterPlotPopup: makeColorMap() - make 255 gray value colors or if pseudocolor mode, then color range
makeInverseMap(int[], int) - Method in class MedianCut: makeInverseMap() - for all cubes, compute centroid of colors in cube.
makeMenuItem(Menu, String, String, int) - Method in class ShowScatterPlotPopup: makeMenuItem() - make menuItem entry in menu list.
makeSubMenu(Menu, String, String, int) - Method in class ShowScatterPlotPopup: makeSubMenu() - make submenu entry in menu list.
masks - Variable in class WriteGifEncoder
math - Variable in class ProtPlot: math package
MathPRP - class MathPRP.: This class contains math functions used for computing statistics in ProtPlot.
MathPRP(ProtPlot) - Constructor for class MathPRP: MathPRP() - constructor for Math package
MAX_COLS - Static variable in class ReadPRP: max # cols in data file
MAX_DISTANCE - Static variable in class Cluster: value to use if no samples exist
MAX_FAMILIES - Static variable in class ProtPlot: max # protein class names
MAX_NEAREST_PROTEINS - Static variable in class ProtPlot: Max # proteins to cluster in similarity cluster plot
MAX_PROTEINS - Static variable in class ProtPlot: maximum # of protein spots ever seen in the union of all .prp DBs
MAX_PRP_FILES - Static variable in class ProtPlot: Max # of PRP databases that may be read at one time
MAX_SAPARAMS - Static variable in class ProtPlot: max # of stand-alone parameters
MAX_SCR_SIZE - Static variable in class ShowScatterPlotPopup: prewired max scroller size
MAX_STEPS_SCR - Static variable in class ShowScatterPlotPopup: prewired scroller steps
MAX_STEPS_SCR2 - Static variable in class ShowScatterPlotPopup: prewired scroller steps
MAX_TISSUES - Static variable in class ProtPlot: max # tissue names
maxbits - Variable in class WriteGifEncoder
maxcode - Variable in class WriteGifEncoder
MAXCODE(int) - Method in class WriteGifEncoder: MAXCODE() - return n bits
MAXCOLORS - Static variable in class MedianCut: maximum # of output colors
maxCols - Variable in class ReadPRP: max size of token array
maxData_MW - Variable in class ReadPRP: range of MW data
maxData_pI - Variable in class ReadPRP: range of pI data
maxDataH - Variable in class StatisticsPRP: max value in data[]
maxExpr - Variable in class ExprProfile: maximum of the sampleData[] values
maxExprVal - Variable in class ProtPlot: Expression range scroller - Expression upper bound [0.0:1.0]
maxFamilies - Variable in class ReadFamilies: max # of families
maxmaxcode - Variable in class WriteGifEncoder
maxPoints - Variable in class DrawProtScatterPlot: max # points allocated for drawing arrays
maxProteins - Variable in class ReadPRP: max # of proteins
maxProteinsFound - Variable in class ProtPlot: maximum # of proteins found in any one sample
maxRatioSample - Variable in class ProtPlot: Expression-ratio (X/Y) range of actual samples- upper bound
maxRatioVal - Variable in class ProtPlot: Expression-ratio (X/Y) range scroller - Ratio upper bound
maxTissues - Variable in class ReadTissues: max # of families
maxX - Variable in class Draw2DprotPlot: range set in initial call
maxXscroll - Variable in class Draw2DprotPlot: range set by ShowPlotPopup scrollers
maxY - Variable in class Draw2DprotPlot: range set in initial call
maxYscroll - Variable in class Draw2DprotPlot: range set by ShowPlotPopup scrollers
mbar - Variable in class ShowScatterPlotPopup: menu bar for GUI
MC_Cube - class MC_Cube.
MC_Cube() - Constructor for class MC_Cube: MC_Cube() - constructor
meanAbsDevH - Variable in class StatisticsPRP: mean absolute deviation
meanExpr - Variable in class ExprProfile: mean expression of the sampleData[] values.
meanH - Variable in class StatisticsPRP: mean of data[]
meanIdx - Variable in class StatisticsPRP: index of mean in hist[]
MedianCut - class MedianCut.: MedianCut converts an RGB image to 8-bit index color using Heckbert's median-cut color quantization algorithm.
MedianCut(int[], int, int) - Constructor for class MedianCut: MedianCut() - Constructor Then call cvtImg24toImg8() to get the 8-bit image.
medianH - Variable in class StatisticsPRP
medianIdx - Variable in class StatisticsPRP: index of median in hist[]
menuFont - Variable in class ShowScatterPlotPopup: Define the menu fonts
menuFontFamily - Variable in class ProtPlot: default menu item font family name
mEPprotList - Variable in class ExprProfileScrollPane: List of mPids being used for EP panel
mEPprotList - Variable in class ShowExprProfilesPopup: Master Protein List being used for EP plots
mExprVect - Variable in class Protein: Master expression list vector [0:nPRPs-1] for this protein NOTE: ONLY used with Master Protein List, it is Null otherwise.
mExprVector - Variable in class Cluster: Master Protein List [0:nMasterPids-1][0:nSamples-1] of protein expression values from all PRP DBs
mExprVector - Variable in class ProtPlot: Master Protein List [0:nMasterPids-1][0:nSamples-1] of protein expression values from all PRP DBs
miChkBoxAccessGenomicDBs - Variable in class ShowScatterPlotPopup: "Access a genomic Web server if you click on a spot [CB]"
miChkBoxAutoUpdateRptMode - Variable in class ShowScatterPlotPopup: "Auto-update reports if the state changes [CB]"
miChkBoxClusterDistAVG_ALL_DATA - Variable in class ShowScatterPlotPopup: "Use average all data distance metric [RB]
miChkBoxClusterDistMAP_LOW_VALUES - Variable in class ShowScatterPlotPopup: "Use map low values distance metric [RB]
miChkBoxClusterDistWEIGHT - Variable in class ShowScatterPlotPopup: "Use weighted distance metric [RB]
miChkBoxDisplayXYscatterplot - Variable in class ShowScatterPlotPopup: "Display (X vs Y) else (Mw vs pI) scatterplot [CB]"
miChkBoxFilterByExprRange - Variable in class ShowScatterPlotPopup: Filter data by expression range [CB]"
miChkBoxFilterByProteinFamily - Variable in class ShowScatterPlotPopup: "Filter data by protein families [CB]"
miChkBoxFilterByTissue - Variable in class ShowScatterPlotPopup: "Filter data by tissues [CB]"
miChkBoxFilterByXY_KStest - Variable in class ShowScatterPlotPopup: "Filter by X & Y sets Kolmogorov-Smirnov-test results [CB]"
miChkBoxFilterByXYmissingProteins - Variable in class ShowScatterPlotPopup: "Filter by X & Y sets missing and > N samples [CB]"
miChkBoxFilterByXYtTest - Variable in class ShowScatterPlotPopup: "Filter by X & Y sets t-test results [CB]"
miChkBoxGenBankServer - Variable in class ShowScatterPlotPopup: "Use GenBank Web server [RB]
miChkBoxLogMW - Variable in class ShowScatterPlotPopup: "Use log of (MW) [CB]"
miChkBoxMouseOver - Variable in class ShowScatterPlotPopup: "Enable mouse-over to see data [CB]"
miChkBoxOutsideRatioRange - Variable in class ShowScatterPlotPopup: "Filter by (X/Y) outside of [minRatioVal:maxRatioVal] sliders"
miChkBoxPIRProClassServer - Variable in class ShowScatterPlotPopup: "Use PIR ProClass Web server [RB]"
miChkBoxReqAtLeastNsamples - Variable in class ShowScatterPlotPopup: "Filter by requiring at least N samples [RB]"
miChkBoxReqAtMostNsamples - Variable in class ShowScatterPlotPopup: "Filter by requiring at most N samples [RB]"
miChkBoxShowClusteredProteins - Variable in class ShowScatterPlotPopup: "Show clustered proteins by black boxes [CB]"
miChkBoxShowExpr - Variable in class ShowScatterPlotPopup: "Show expression data else just position [CB]"
miChkBoxShowFilterResults - Variable in class ShowScatterPlotPopup: "Show filter results [CB]"
miChkBoxShowXandYsamplesMode - Variable in class ShowScatterPlotPopup: "Show both X and Y samples if doing X/Y filtering [CB]"
miChkBoxSortAssendingRptMode - Variable in class ShowScatterPlotPopup: "Sort report assending order[CB]"
miChkBoxSwissProtServer - Variable in class ShowScatterPlotPopup: "Use Swiss-Prot Web server [RB] "
miChkBoxUseCmapRatioMode - Variable in class ShowScatterPlotPopup: "Show samplesX/sampleY ratio range color map [RB]"
miChkBoxUseEPsetExprDataMode - Variable in class ShowScatterPlotPopup: "Show current sample expression data [RB]"
miChkBoxUseExprDataMode - Variable in class ShowScatterPlotPopup: "Show current sample expression data [RB]"
miChkBoxUseExprPlotMode - Variable in class ShowScatterPlotPopup: "Popup Expression Profile plots [CB]"
miChkBoxUseLocalDoc - Variable in class ShowScatterPlotPopup: "Use local documentation else ProtPlot server"
miChkBoxUsePseudocolor - Variable in class ShowScatterPlotPopup: "Use pseudocolor else grayscale for expression [CB]
miChkBoxUseRGratioMode - Variable in class ShowScatterPlotPopup: "Show X-samples/Y-sample ratio (Red=X + Green=Y) data [RB]"
miChkBoxUseSavedClusterSet - Variable in class ShowScatterPlotPopup: "Filter by AND of Saved Clustered proteins [CB]"
miChkBoxUseSavedFilterSet - Variable in class ShowScatterPlotPopup: "Filter by AND of Saved Filtered proteins [CB]"
miChkBoxUseTotPRPfiles - Variable in class ShowScatterPlotPopup: "Build DB from XXX_tot.prp files else from XXX_under200k.prp files"
miChkBoxUseVarRadiusExpr - Variable in class ShowScatterPlotPopup: "Use radius proportional to expression else constant [CB]"
miChkBoxUseXYSetCmapRatioMode - Variable in class ShowScatterPlotPopup: "Show X-Set-samples /X-Set-samples ratio range color map [RB]"
miClustSimilar - Variable in class ShowScatterPlotPopup: MenuItem for "Cluster similar proteins to current protein by EP profile"
miEPmissing - Variable in class ShowScatterPlotPopup: MenuItem for ""Report EP set statistics of proteins passing missing protein filter"
MIN_CANVAS_HEIGHT - Static variable in class Draw2DprotPlot
MIN_CANVAS_HEIGHT - Static variable in class ExprProfileCanvas: default canvas height size
MIN_CANVAS_WIDTH - Static variable in class Draw2DprotPlot
MIN_CANVAS_WIDTH - Static variable in class ExprProfileCanvas: default canvas width size
MIN_COLS - Static variable in class ExprProfileScrollPane: minimum # of columns for the grid
MIN_ROWS - Static variable in class ExprProfileScrollPane: minimum # of rows for the grid
minData_MW - Variable in class ReadPRP: range of MW data
minData_pI - Variable in class ReadPRP: range of pI data
minDataH - Variable in class StatisticsPRP: min value in data[]
minExpr - Variable in class ExprProfile: minimum of the sampleData[] values
minExprVal - Variable in class ProtPlot: Expression range scroller - Expression lower bound [0.0:1.0]
minRatioSample - Variable in class ProtPlot: Expression-ratio (X/Y) range of actual samples - lower bound
minRatioVal - Variable in class ProtPlot: Expression-ratio (X/Y) range scroller - Ratio lower bound
minX - Variable in class Draw2DprotPlot: range set in initial call
minXscroll - Variable in class Draw2DprotPlot: range set by ShowPlotPopup scrollers
minY - Variable in class Draw2DprotPlot: range set in initial call
minYscroll - Variable in class Draw2DprotPlot: range set by ShowPlotPopup scrollers
miPrevPlotCB - Variable in class ShowScatterPlotPopup: Last Show Plot mode for use in toggling XY set checkbox
miXYmissing - Variable in class ShowScatterPlotPopup: MenuItem for "Report X&Y sets statistics of proteins passing missing protein filter"
mNbr - Variable in class ExprProfileScrollPane: .mList[mNbr] in database to display
mnEPdata - Variable in class Filter: computed mean intensity EP set data for current protein
mnX - Static variable in class MathPRP: RTN: mean X
mnXdata - Variable in class Filter: computed mean intensity X set data for current protein
mnY - Static variable in class MathPRP: RTN: mean Y
mnYdata - Variable in class Filter: computed mean intensity Y set data for current protein
mode - Variable in class ShowStringPopup: mode of operation used in creating this window.
MODE_CIRCLE - Static variable in class ExprProfileCanvas: draw circles for each entry
MODE_CURVE - Static variable in class ExprProfileCanvas: draw continuous curve
MODE_LINE - Static variable in class ExprProfileCanvas: draw vertical bars
modeH - Variable in class StatisticsPRP: mode of data[]
modeIdx - Variable in class StatisticsPRP: index of mode in hist[]
mouseClicked(MouseEvent) - Method in class Draw2DprotPlot
mouseClicked(MouseEvent) - Method in class ExprProfilePanel
mouseClicked(MouseEvent) - Method in class ShowScatterPlotPopup: mouseClicked() - handle mouse Click events
mouseDragged(MouseEvent) - Method in class Draw2DprotPlot
mouseDragged(MouseEvent) - Method in class ExprProfilePanel: mouseDragged() - just report (Sample, expr) of nearest sample near where mouse is
mouseDragged(MouseEvent) - Method in class ShowScatterPlotPopup: mouseDragged() - handle mouse Drag events
mouseEntered(MouseEvent) - Method in class Draw2DprotPlot
mouseEntered(MouseEvent) - Method in class ExprProfilePanel
mouseEntered(MouseEvent) - Method in class ShowScatterPlotPopup: mouseEntered() - handle mouse Enter events
mouseExited(MouseEvent) - Method in class Draw2DprotPlot
mouseExited(MouseEvent) - Method in class ExprProfilePanel
mouseExited(MouseEvent) - Method in class ShowScatterPlotPopup: mouseExited() - handle mouse Exit events
mouseHandler(int, int, int, boolean) - Method in class DrawProtScatterPlot: mouseHandler() - interact with current plot if a graphic plot.
mouseMoved(MouseEvent) - Method in class Draw2DprotPlot: mouseMoved() - process mouse event - update MouseOver
mouseMoved(MouseEvent) - Method in class ExprProfilePanel
mouseMoved(MouseEvent) - Method in class ShowScatterPlotPopup: mouseMoved() - handle mouse Move events
mouseOverCheckBox - Variable in class ShowScatterPlotPopup: Show Mouse-over info
mousePressed(MouseEvent) - Method in class Draw2DprotPlot: mousePressed() - process mouse event, change current clone
mousePressed(MouseEvent) - Method in class ExprProfilePanel: mousePressed() - handle mouse Pressed events
mousePressed(MouseEvent) - Method in class ShowScatterPlotPopup: mousePressed() - handle mouse Press events
mouseReleased(MouseEvent) - Method in class Draw2DprotPlot
mouseReleased(MouseEvent) - Method in class ExprProfilePanel: mouseReleased() - handle mouse Released events
mouseReleased(MouseEvent) - Method in class ShowScatterPlotPopup: mouseReleased() - handle mouse Release events
mPid - Variable in class ExprProfile: ARG: Master Protein ID (pid) for gene we are creating if != -1
mPid - Variable in class Protein: Master PID cross reference to global list of proteins index kept in prp.mPidList[].
mPid2PidMap - Variable in class ProtPlot: Map of mPids to pids for specific samples [0:nMasterPids-1][0:nSamples-1].
mPidFiltered - Variable in class ProtPlot: Is list [0:nMpidFiltered] of all mPids that passed the data filter and are used by the current sample (for a single sample) or by a set of samples (e.g.
mPidI - Variable in class Cluster: current mPid i
mPidJ - Variable in class Cluster: current mPid J
mPidSamples - Variable in class ProtPlot: Is list [0:nMpidSamples] of all mPids used by the current sample (for a single sample) or by a set of samples (e.g.
mPidSimilarCluster - Variable in class ProtPlot: List [0:nMpidSimilarCluster-1] of mPids similar to the current protein curMPID
mProtList - Variable in class ProtPlot: Master Protein List [0:nMasterPids-1] of proteins from all PRP databases indexed by mPid value.
mProtSwissProtAcc - Variable in class ProtPlot: Master Protein List [0:nMasterPids-1] of protein SWISS-PROT Acc #s from all PRP DBs is indexed by mPid value.
mProtSwissProtId - Variable in class ProtPlot: Master Protein List [0:nMasterPids-1] of protein IDs from all PRP DBs is indexed by mPid value.
mReady - Variable in class ProtPlot: ready to analyze
mStatus - Static variable in class UtilPRP
mw - Variable in class Protein: molecular mass

N

n_bits - Variable in class WriteGifEncoder
N_EP_PROTEINS - Variable in class ExprProfileScrollPane
nBinsH - Variable in class StatisticsPRP: 0 if none.
nBoth - Variable in class Cluster: # of samples in both mPidI and mPidJ in current expr profile sample list
nbrProteins - Variable in class ProtPlot: List of # proteins/sample [0:nPRPs-1]
nbrProteinsLabel - Variable in class ShowScatterPlotPopup: "# proteins/sample threshold"
nbrProteinsThrSlider - Variable in class ShowScatterPlotPopup: Number of proteins/samples threshold slider
nbrProteinsValueLabel - Variable in class ShowScatterPlotPopup: "# proteins/sample threshold"
nbrSamplesLabel - Variable in class ShowScatterPlotPopup: "# samples threshold"
nbrSamplesThrSlider - Variable in class ShowScatterPlotPopup: Number of samples threshold slider
nbrSamplesValueLabel - Variable in class ShowScatterPlotPopup: "# samples threshold" value
nCols - Variable in class ExprProfileScrollPane: # of columns in the Grid
nCols - Variable in class ReadPRP: actual # of tokens found
nCols - Variable in class ShowStringPopup: # of character cols to show
ncubes - Variable in class MedianCut: # of color cubes
nEP - Variable in class Filter: # of EP set members after setup
nEPpresent - Variable in class ExprProfile: # of sample's in subset to plot that don't have 0.0 expression
nEPproteins - Variable in class ExprProfileScrollPane: # genes to display in popup EP plot
nEPsamples - Variable in class ExprProfile: # of sample's to draw after setup
nEPsamplesPassedMinProteins - Variable in class Filter: Compute the min # of EP set samples passing > S proteins/Sample test
NEVER - Static variable in class ProtPlot: Always FALSE
newProteinCopy() - Method in class Protein: newProteinCopy() - make a new copy of this Protein instance.
nextID - Static variable in class MC_Cube
nextPid - Static variable in class Protein: id of this protein instance
nextZoomMag(int, int) - Static method in class UtilPRP: nextZoomMag() - modulo 1X, 2X, 5X, 10X, 20X, 30X, 40X, 50X,
nFamilies - Variable in class PopupFamilyNameSelector: # of Families
nFamilies - Variable in class Protein: prc.rc.nFamilies
nFamilies - Variable in class ReadFamilies: # of families
nFields - Variable in class ReadPRP: # of fields in actual data file
nGridElements - Variable in class ExprProfileScrollPane: i.e.
nHP_E - Variable in class ExprProfileScrollPane: # of HPS in an Expr Profile
nMasterPids - Variable in class ProtPlot: Number of proteins in the Master Protein List mPid[]
nMissing - Variable in class Cluster: # of missing samples in either mPidI or mPidJ in current expr profile sample list
nMpidFiltered - Variable in class ProtPlot: size of mPidSamples[] list.
nMpidSamples - Variable in class ProtPlot: size of mPidSamples[] list.
nMpidSimilarCluster - Variable in class ProtPlot: # of clustered proteins
noArgsFlag - Variable in class ProtPlot: set if there are no args specified
nOptions - Variable in class PopupDialogQuery: optionValues[0:nOptions]
normFont - Variable in class Draw2DprotPlot: The normal font
normToOneFlag - Variable in class ExprProfile: flag: normalize sampleData[] to 1.0
notOkColor - Variable in class Draw2DprotPlot
nOverDaltonLimit - Variable in class ProtPlot: Number of proteins found that are > 200K daltons
nPoints - Variable in class ExprProfileScrollPane: nProteins*nHP_E
nPointsMax - Variable in class Draw2DprotPlot: maximum drawing list size.
nPointsPlotted - Variable in class Draw2DprotPlot: # points plotted after data is filtered
nProteins - Variable in class ExprProfileScrollPane: # genes in exprProfileCL
nProteins - Variable in class ReadPRP: actual # of proteins found
nProteins - Variable in class ShowExprProfilesPopup: # of genes in expression profile
nPRPs - Variable in class Cluster: # of samples in entire DB
nPRPs - Variable in class GetListOfPRPs: # of files read
nPRPs - Variable in class ProtPlot: # of PRP file names
nr_betacf(double, double, double) - Static method in class MathPRP: nr_betacf() - evaluation fct for the incomplete Beta function 'x(a,b).
nr_betai(double, double, double) - Static method in class MathPRP: nr_betai() - return the incomplete Beta function 'x(a,b).
nr_gammln(double) - Static method in class MathPRP: nr_gammln() - Return ln(gamma()) of x by polynomial evaluation.
nr_kstwo(double[], int, double[], int) - Static method in class MathPRP: nr_kstwo() - Kolmogorov-Smirnov statistic D and the compute the probability of the null hypothesis of 2 bins of data.
nr_probks(double) - Static method in class MathPRP: nr_probks() - Calc Kolmogorov-Smirnov probability qKS.
nr_sort(int, double[]) - Static method in class MathPRP: nr_sort() - quick-sort of bin of data[0:n-1] in assend.
nRows - Variable in class ExprProfileScrollPane: # of rows in the Grid
nRows - Variable in class ShowStringPopup: # of character rows to show
nSampleEPlist - Variable in class ProtPlot: # of samples used in the expression vector sampleEPlist[0:nPRPs-1]
nSamples - Variable in class Cluster: # of samples in current expr profile sample list
nSamples - Variable in class ProtPlot: Number of ReadPRP instances of PRP databases
nSamples - Variable in class Protein: # of samples with this protein - ONLY used by master list
nSamplesPassedMinProteins - Variable in class Filter: Compute the min # of X&Y or EP set samples passing > S proteins/Sample test
nSampleXlist - Variable in class ProtPlot: # of samples used in the X set sampleXlist[0:nPRPs-1]
nSampleYlist - Variable in class ProtPlot: # of samples used in the Y set sampleYlist[0:nPRPs-1]
nSAparam - Static variable in class ProtPlot: # of stand-alone params
nSavedClusterMPIDs - Variable in class ProtPlot: # of saved clustered proteins
nSavedFilterMPIDs - Variable in class ProtPlot: # of saved Filtered proteins
nStateEntries - Static variable in class UtilPRP: # of (name,value) pairs read from the "protplot.prpstate" file
nTissues - Variable in class PopupTissueNameSelector: # of tissues
nTissues - Variable in class Protein: prc.rt.nTissues
nTissues - Variable in class ReadTissues: # of families
numPixels - Variable in class WriteGifEncoder
nX - Variable in class Filter: # of X set members after setup
nXsamplesPassedMinProteins - Variable in class Filter: Compute the min # of X set samples passing > S proteins/Sample test
nXY - Static variable in class MathPRP: RTN: if calcXYstat
nY - Variable in class Filter: # of Y set members after setup
nYsamplesPassedMinProteins - Variable in class Filter: Compute the min # of Y set samples passing > S proteins/Sample test

O

oGifFileName - Variable in class Draw2DprotPlot: GIF output file if used
oGifFileName - Variable in class ExprProfileCanvas: full Gif file path name
ok - Variable in class PopupPRPlistSelector: pressed close and the proper number of samples expected was set
ok - Variable in class WriteGifEncoder: 80% occupancy
okBetaCF - Static variable in class MathPRP: RTN: if nr_betacf() was ok
okBetaI - Static variable in class MathPRP: RTN: if nr_betai() was ok
okColor - Variable in class Draw2DprotPlot
okProbKS - Static variable in class MathPRP: RTN: if nr_probks() was ok
oldSample - Variable in class PopupPRPlistSelector: old Sample if selecting a single sample (-1 if none)
oldSampleList - Variable in class PopupPRPlistSelector: old list of samples [0:oldNlist-1]
openProteinSetFile(String) - Method in class ShowScatterPlotPopup: openProteinSetFile() - open up a protein set database file.
optionChoice - Variable in class PopupDialogQuery: opt.
optionPanel - Variable in class PopupDialogQuery: for options
optionValues - Variable in class PopupDialogQuery: list of option values if present
optReportMode - Variable in class ShowStringPopup: Optional Report mode if > 0
osName - Static variable in class ProtPlot: operating system Windows, SUNOS, etc
output(int, FileOutputStream) - Method in class WriteGifEncoder: output() - Output the given code.
outsideRatioRangeFlag - Variable in class ProtPlot: Filter by (X/Y) of samples X & samples Y outside of [minRation:maxRatio] sliders

P

paint(Graphics) - Method in class Draw2DprotPlot: paint() - draw the expression profile
paint(Graphics) - Method in class ExprProfileCanvas: paint() - draw the expression profile in canvas if a legal protein mPid.
paint(Graphics) - Method in class ExprProfilePanel: paint() - draw the expression profile plot only repaint if a legal protein mPid.
paint(Graphics) - Method in class ExprProfilePopup: paint() - repaint buttons and canvas
paint(Graphics) - Method in class ExprProfileScrollPane: paint() - redraw plots near selected Row.
paint(Graphics) - Method in class ShowExprProfilesPopup: paint() - repaint by causes the ExprProfileScrollPane to repaint.
paint(Graphics) - Method in class ShowScatterPlotPopup: paint() - repaint subwindows
panelHeight - Variable in class ShowScatterPlotPopup: default size - must be set here!
panelWidth - Variable in class ShowScatterPlotPopup: default size - must be set here!
parseDelimChar - Variable in class UtilPRP: current delim of "name(delim)value" pair
parseName - Variable in class UtilPRP: current name of "name=value" pair
parseRows(String) - Method in class ReadFamilies: parseRows() - parse and save a rows of data in rd.protList[] data structures.
parseRows(String) - Method in class ReadTissues: parseRows() - parse and save a rows of data in rd.protList[] data structures.
parseRows(String, int) - Method in class ReadPRP: parseRows() - parse & save a rows of data in rd.protList[] data structures.
parseValue - Variable in class UtilPRP: current value of "name=value" pair
passedDisplayXYRangeTest - Variable in class Filter: set if doing display X vs Y in ratio mode AND (exprX,exprY) in X and Y range of scatterplot
passedEPminSamplesCtr - Variable in class Filter: counters for missing samples protein test for EP set
passedExprCtr - Variable in class Filter: counters Expr counter
passedFamilyCtr - Variable in class Filter: counters Family counter
passedFilterCtr - Variable in class Filter: counters Filter counter
passedKStestCtr - Variable in class Filter: counters for KS-test
passedMaxMWsizeCtr - Variable in class Filter: counters max MW size counter
passedMissingProteins - Variable in class Filter: Combined flag for both X & Y or EP missing proteins tests
passedMwPIRangeCtr - Variable in class Filter: counter for test of (pM.pI,pM.mw) within pI and Mw scroller range limits
passedMwPIRangeTest - Variable in class Filter: Flag that tests if (pM.pI,pM.mw) is within the pI and Mw scroller range limits
passedNsamplesCtr - Variable in class Filter: counters N samples counter
passedRatioCtr - Variable in class Filter: counters Ratio counter
passedSavedClusterCtr - Variable in class Filter: counter for proteins in saved Cluster set of proteins
passedSavedFilterCtr - Variable in class Filter: counter for proteins in saved Filter set of proteins
passedTissueCtr - Variable in class Filter: counters Tissue counter
passedTtestCtr - Variable in class Filter: counters for t-test
passedXYmissingProteinsCtr - Variable in class Filter: counter for missing X and Y set protein test
pdq - Variable in class ShowScatterPlotPopup: hidden popup dialog
pF - Variable in class StatisticsPRP: CALC: f-test p-value w/NULL hypoth
pfns - Variable in class ShowScatterPlotPopup: Popup tissue name selector window created when needed
phelp - Variable in class ShowScatterPlotPopup: Popup help window
pI - Variable in class Protein: isoelectric point
pid - Variable in class Protein: local index
pixelIndex - Variable in class WriteGifEncoder
pixels - Variable in class WriteGifEncoder
pixels32 - Variable in class MedianCut: 32-bit image[width*height] (Alpha,Red,Green,Blue) pixels
pixels8 - Variable in class MedianCut: 8-bit image[width*height] using LUTs
pKS - Variable in class StatisticsPRP: CALC: Kolmogorov-Smirnov test p-value w/NULL hypoth
plotStyleButton - Variable in class ExprProfilePopup: plot style (line, circle, curve) button
plotStyleButton - Variable in class ShowExprProfilesPopup
plotStyleMode - Variable in class ExprProfileCanvas: plot mode style: 0=line, 1=circle, 2=curve
plotStyleMode - Variable in class ExprProfileScrollPane: plot style mode: 0=line, 1=circle, 2=curve
plotStyleMode - Variable in class ShowExprProfilesPopup: Mode for plotting points in the expr profile where: 0=(bar) line, 1=circle, 2=curve
pointColor - Variable in class Draw2DprotPlot
POPUP_HEIGHT - Static variable in class ShowScatterPlotPopup: Height of main window
POPUP_WIDTH - Static variable in class ShowScatterPlotPopup
popupAlertMsg(String) - Method in class UtilPRP: popupAlertMsg() - popup ALERT message and then timeout.
popupClusterWindowFlag - Static variable in class Cluster: flag set it popup cluster control window GUI
PopupDialog - class PopupDialog.: Class PopupDialog pops up a dialog box for error msgs, warnings, etc.
PopupDialog.MainDialog - class PopupDialog.MainDialog.: MainDialog() - Class extends Dialog class.
PopupDialog.MainDialog(PopupDialog, Frame, String, boolean, boolean, Color) - Constructor for class PopupDialog.MainDialog: MainDialog() - create dialog box with Yes & No buttons
PopupDialog.MainDialog(PopupDialog, Frame, String, boolean, Color) - Constructor for class PopupDialog.MainDialog: MainDialog() - create dialog box with OK button
PopupDialog(String) - Constructor for class PopupDialog: PopupDialog() - create dialog box with OK button
PopupDialog(String, boolean) - Constructor for class PopupDialog: PopupDialog() - create dialog box with yes & no buttons
PopupDialogQuery - class PopupDialogQuery.: The class is a generic popup query dialog window used throughout ProtPlot.
PopupDialogQuery(ProtPlot, Frame, int) - Constructor for class PopupDialogQuery: PopupDialogQuery() - Constructor
PopupFamilyNameSelector - class PopupFamilyNameSelector.: Class PopupFamilyNameSelector .java - popup protein family name selection This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government and Djamel Medjahed (SAIC-Frederick).
PopupFamilyNameSelector(ProtPlot, ShowScatterPlotPopup) - Constructor for class PopupFamilyNameSelector: PopupFamilyNameSelector() - popup selector for family name(s)
popupName - Variable in class ShowExprProfilesPopup
popupPropertyBits - Variable in class ShowExprProfilesPopup: ARG: for PopupRegistry
PopupPRPlistSelector - class PopupPRPlistSelector.: This class creates and displays a popup window to select samples.
PopupPRPlistSelector(ProtPlot, ShowScatterPlotPopup, int, int, boolean[], boolean) - Constructor for class PopupPRPlistSelector: PopupPRPlistSelector() - popup selector
PopupStatusWindow - class PopupStatusWindow.: Class PopupStatusWindow.java - popup a status window.
PopupStatusWindow(ProtPlot, boolean) - Constructor for class PopupStatusWindow: PopupStatusWindow() - popup status window
PopupTissueNameSelector - class PopupTissueNameSelector.: Class PopupTissueNameSelector .java - popup window to define tissue names This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government and Djamel Medjahed (SAIC-Frederick).
PopupTissueNameSelector(ProtPlot, ShowScatterPlotPopup) - Constructor for class PopupTissueNameSelector: PopupTissueNameSelector() - popup selector for tissue name(s)
popupViewer(URL, String, String) - Method in class UtilPRP: popupViewer() - popup another web browser for the help HTML file.
ppns - Variable in class ShowScatterPlotPopup: popup PRP list name selector window created when needed
preferredHeight - Variable in class Draw2DprotPlot: target Size for selecting a line
preferredHeight - Variable in class ExprProfileCanvas: preferred canvas height size
preferredHeight - Variable in class ExprProfilePopup: prefered height canvas size, 0 to use defaults
preferredWidth - Variable in class Draw2DprotPlot: target Size for selecting a line
preferredWidth - Variable in class ExprProfileCanvas: preferred canvas width size
preferredWidth - Variable in class ExprProfilePopup: prefered width canvas size, 0 to use defaults
prevBestMPID - Variable in class DrawProtScatterPlot: previus best mPid of protein selected by mouse motion or clicking
prjPRPdir - Static variable in class ProtPlot: standalone startup PRP/ Directory
PRO_CLASS_BASE_URL - Static variable in class ProtPlot
probKS - Static variable in class MathPRP: RTN: probability of null hypoth same distrib
proClassServerBase - Variable in class ProtPlot: PIR lookup on our server
promptDir - Static variable in class ExprProfilePopup: last prompted directory for popup dialog
promptDir - Static variable in class ShowScatterPlotPopup: last prompted directory for popup dialog
promptExt - Static variable in class ExprProfilePopup: for FilenameFilter file extension for popup dialog
promptExt - Static variable in class ShowScatterPlotPopup: for FilenameFilter file extension for popup dialog
promptFile - Static variable in class ExprProfilePopup: last prompted project for popup dialog
promptFile - Static variable in class ShowScatterPlotPopup: last prompted project for popup dialog
promptFileName(String, String, String, String, String, boolean, boolean) - Method in class ShowScatterPlotPopup: promptFileName() - dialog prompt for file name.
prot - Variable in class ProtPlot: Clone instances
Protein - class Protein.: Class Protein represents an individual Protein spot entry.
Protein() - Constructor for class Protein: Protein() - constructor tomake an empy instance
Protein(float, float, String, String, String, long, long, float) - Constructor for class Protein: Protein() - constructor for new instance.
Protein(ProtPlot) - Constructor for class Protein: Protein() - constructor to set prp - MUST BE CALLED FIRST!!!
protList - Variable in class ReadPRP: [0:nProteins-1] list of all proteins
ProtPlot - class ProtPlot.: Class ProtPlot.java is the main class.
PROTPLOT_STATE_FILE - Static variable in class ProtPlot: name of the ProtPlot state file
ProtPlot() - Constructor for class ProtPlot
protPlotStateHT - Variable in class ProtPlot: Hash table of the ProtPlot state read from stateFile ".prpstate" if not null
protServerBase - Variable in class ProtPlot: top level codebase for ProtPlot server
prp - Static variable in class Cluster: instance of ProtPlot
prp - Variable in class Draw2DprotPlot: instance of ProtPlot
prp - Variable in class DrawProtScatterPlot: instance of ProtPlot
prp - Variable in class EventHandlerPRP: instance of ProtPlot
prp - Variable in class ExprProfile: link to global prpxplorer instance
prp - Variable in class ExprProfileCanvas: instance of ProtPlot so we can clear flags indicating the user did a manual quit()
prp - Variable in class ExprProfilePanel: link to global prpxplorer instance
prp - Variable in class ExprProfilePopup: link to global ProtPlot instance
prp - Variable in class ExprProfileScrollPane: link to global ProtPlot instance
prp - Variable in class FileIOPRP: instance of ProtPlot
prp - Variable in class Filter: instance of ProtPlot
prp - Variable in class GetListOfPRPs: instance of ProtPlot
prp - Static variable in class MathPRP: instance of ProtPlot
prp - Variable in class PopupDialogQuery: link to global instance to prpxplorer
prp - Variable in class PopupFamilyNameSelector
prp - Static variable in class PopupPRPlistSelector
prp - Variable in class PopupStatusWindow
prp - Variable in class PopupTissueNameSelector
prp - Static variable in class Protein: instance of ProtPlot
prp - Variable in class ReadFamilies: instance of ProtPlot
prp - Variable in class ReadPRP: instance of ProtPlot
prp - Variable in class ReadTissues: instance of ProtPlot
prp - Variable in class ReportPRP: instance of ProtPlot
prp - Variable in class ShowExprProfilesPopup
prp - Variable in class ShowScatterPlotPopup: instance of ProtPlot
prp - Variable in class ShowStringPopup: link to global ProtPlot instance
prp - Static variable in class StatisticsPRP: instance of ProtPlot
prp - Static variable in class UtilPRP: instance of ProtPlot
prpDir - Variable in class ReadPRP: Directory of the .prp data file to use
prpEndsWith - Variable in class GetListOfPRPs: optional end of file name to restrict which files are read
prpFile - Variable in class ReadPRP: File of the .prp data file to use
prpFileNames - Variable in class GetListOfPRPs: List of PRP file names [0:nPRPs-1]
prpFileNames - Variable in class ProtPlot: List of PRP file names [0:nPRPs-1]
prpListANDCheckBox - Variable in class PopupPRPlistSelector: select BOTH family and Checkbox
prpListFrame - Variable in class PopupPRPlistSelector: Frame of name checkboxes
prpListNameCheckbox - Variable in class PopupPRPlistSelector: [0:nFamilies-1] checkboxes
prpListNamesFile - Variable in class ProtPlot: File containing the list of .prp files to use
prpName - Variable in class ReadPRP: Name of the .prp data file without .prp and cvt '_' to " "
prpNames - Variable in class GetListOfPRPs: List of PRP names [0:nPRPs-1]
prpNames - Variable in class ProtPlot: List of PRP names [0:nPRPs-1]
pT - Variable in class StatisticsPRP: CALC: t-test p-value w/NULL hypoth
ptns - Variable in class ShowScatterPlotPopup: Popup tissue name selector window created when needed
Putbyte(byte, FileOutputStream) - Method in class WriteGifEncoder: Putbyte() - Write out a byte to the GIF file
Putword(int, FileOutputStream) - Method in class WriteGifEncoder: Putword() - Write out a word to the GIF file
pValue - Variable in class Filter: computed Computed pValue when use the t-Test for current protein
pValueLabel - Variable in class ShowScatterPlotPopup: "P-value threshold"
pValueThr - Variable in class ProtPlot: The p-Value threshold slider value in the range of 0.0 to 1.0
pValueThrSlider - Variable in class ShowScatterPlotPopup: pValue threshold slider
pValueThrUB - Variable in class ProtPlot: (pValue Threshold) Vertical slider initial value Upper Bound
pValueValueLabel - Variable in class ShowScatterPlotPopup: "P-value threshold" value

Q

quickSort(int[], int, int) - Method in class MedianCut: quickSort() - sort the map Based on the QuickSort method by James Gosling from Sun's SortDemo applet
quit() - Method in class ExprProfilePopup: quit() - dispose of this object
quit() - Method in class PopupFamilyNameSelector: quit() - kill this frame
quit() - Method in class PopupPRPlistSelector: quit() - kill this frame
quit() - Method in class PopupTissueNameSelector: quit() - kill this frame
quit() - Method in class ProtPlot: quit() - kill this application
quit() - Method in class ShowStringPopup: quit() - closing down the window, get rid of the frame.
quitButton - Variable in class PopupStatusWindow: quit the application button

R

r - Variable in class WriteGifEncoder
radius - Variable in class Draw2DprotPlot
RADIUS - Static variable in class Draw2DprotPlot
ratioValLB - Variable in class ProtPlot: (Expression-ratio) Vertical slider (sX/xY ratio) initial value Lower Bound
ratioValUB - Variable in class ProtPlot: (Expression-ratio) Vertical slider (sX/xY ratio) initial value Upper Bound
ratioXYsets - Variable in class Filter: computed ratio of mnXdata/mnYdata if mnYdata NEQ 0 for current protein
rColor - Variable in class ShowScatterPlotPopup: [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.
rd - Variable in class Draw2DprotPlot: instance of ReadPRP
rd - Variable in class DrawProtScatterPlot: instance of ReadPRP of current sample
rdList - Variable in class ProtPlot: List [0:nSamples-1] of ReadPRP instances of PRP databases
rdX - Variable in class DrawProtScatterPlot: instance of ReadPRP of ratio sample X
rdY - Variable in class DrawProtScatterPlot: instance of ReadPRP of ratio sample Y
readBytesFromURL(String, String) - Method in class UtilPRP: readBytesFromURL() - read binary data from URL
readData(String, String) - Method in class FileIOPRP: readData() - read data from URL or file depending on prefix.
readDataFile(String) - Method in class ReadPRP: readDataFile() - read (pI,mw,SP-ID) into data structure
readEntirePRPdatabase() - Method in class ProtPlot: readEntirePRPdatabase() - read the entire database.
ReadFamilies - class ReadFamilies.: Class ReadFamilies.java - read protein families file mapping protein families to bit #s.
ReadFamilies(ProtPlot, String, int, String) - Constructor for class ReadFamilies: ReadFamilies() - constructor
readFamiliesFile(String) - Method in class ReadFamilies: readFamiliesFile() - read list of Families into data structure
readFileFromDisk(String) - Method in class FileIOPRP: readFileFromDisk() - Will read file from disk & returns as String Return null if failed.
readFileFromUrl(String) - Method in class FileIOPRP: readFileFromUrl() - read data from http URL, using JavaCGIBridge If the code has "\r\n", then map them to "\n".
readNamedProteinSet(String, String) - Method in class UtilPRP: readNamedProteinSet() - read named protein set file and save it Cluster or Filter Save list.
ReadPRP - class ReadPRP.: Class ReadPRP.java - read a .prp file and set up data structures.
ReadPRP(ProtPlot, String, String, int, int, String, boolean) - Constructor for class ReadPRP: ReadPRP() - constructor to read and build a sample data structure.
readState(String) - Method in class UtilPRP: readState() - read the ProtPlot State file stateFile
ReadTissues - class ReadTissues.: Class ReadTissues.java - read tissues file mapping tissues to bit #s.
ReadTissues(ProtPlot, String, int, String) - Constructor for class ReadTissues: ReadTissues() - constructor
readTissuesFile(String) - Method in class ReadTissues: readTissuesFile() - read list of tissues into data structure
recalcEPsampleIdxLists() - Method in class ProtPlot: recalcEPsampleIdxLists() - recompute the idxSampleEPlist[] NOTE: this does NOT use the #proteins/sample sizing.
recalcXYsampleIdxLists() - Method in class ProtPlot: recalcXYsampleIdxLists() - recompute idxSampleXlist[] & idxSampleYlist[] NOTE: this does NOT use the #proteins/sample sizing.
redBits(int) - Method in class MedianCut: redBits() - Get 8-bit red component of a 15-bit color 8-bit pixel with low 3 bits zero.
reorderColors(int[], int, int, int) - Method in class MedianCut: reorderColors() - Change ordering of 5-bit colors in each word of int[] so we can sort on the 'longDim' color
ReportPRP - class ReportPRP.: Class ReportPRP.java - popup various reports.
ReportPRP(ProtPlot) - Constructor for class ReportPRP: ReportPRP() - constructor
requireAtLeastNsamplesFlag - Variable in class ProtPlot: "Filter by requiring at least N samples [RB]" checkbox for thresholdNsamples
requireAtMostNsamplesFlag - Variable in class ProtPlot: "Filter by requiring at most N samples [RB]" checkbox for thresholdNsamples
resetDefaultstate(boolean) - Method in class ProtPlot: resetDefaultstate() - Reinitialize global user state Anything in this method should be able to be set during runtime from the "Reset" menu.
resetFilterCounters() - Method in class Filter: resetFilterCounters() - reset the filter counters
resetNextPID() - Static method in class Protein: resetNextPID() - clear the next PID counter.
restoreColorOrder(int[], int, int, int) - Method in class MedianCut: restoreColorOrder() - Restore the 5-bit colors to original order
rf - Variable in class PopupFamilyNameSelector
rf - Variable in class ProtPlot: ReadFamilies
rgb - Variable in class WriteGifEncoderHashitem
rgb15(int) - Method in class MedianCut: rgb15() - convert from 24-bit (ignore alpha) to 15-bit color.
rLUT - Variable in class MedianCut: [0:255] Red Color map look up table
rMap - Variable in class ShowScatterPlotPopup: [TODO] The non-linear mapping (typically exponential) from [0:255] to [0.01 : 10.0].
rmax - Variable in class MC_Cube
rmin - Variable in class MC_Cube
rpt - Variable in class EventHandlerPRP: instance of ReportPRP
rpt - Variable in class ProtPlot: instance of ReportPRP
rpt - Variable in class ShowScatterPlotPopup: instance of ReportPRP
RPT_MODE_SIMILAR_CLUSTER - Static variable in class ShowStringPopup: Similar Cluster report with "Cluster Threshold" slider, and "Expr Profile" button
RPT_MODE_SIMPLE - Static variable in class ShowStringPopup: Simple report with "Save As" and "Close" buttons
rptPopup - Static variable in class ProtPlot: Current report string popup instance.
rptType - Variable in class ShowStringPopup: Type of report: "Help", "FilterRpt", "EPFilterRpt", "XYEPmissingRpt", "EPsamplesRpt", "StateRpt", "SampleAssignRpt", "SampleNbrsRpt", "SimClusterRpt",
rSq - Static variable in class MathPRP: RTN: correlation coefficient
rt - Variable in class PopupTissueNameSelector
rt - Variable in class ProtPlot: ReadTissues

S

sampleChoice - Variable in class ShowScatterPlotPopup: Choice selector for setting sample lists
sampleData - Variable in class ExprProfile: normalized quantified data for all sample-E samples
sampleDataNbr - Variable in class ExprProfile: opt.
sampleEPlist - Variable in class ProtPlot: list of samples used in the expression vector [0:nPRPs-1]
sampleLabel - Variable in class ExprProfile: (sampleName,sampleData) sample-E samples
sampleList - Variable in class PopupPRPlistSelector: list of samples in the expression list of of samples [0:prp.nPRPs-1]
sampleName - Variable in class ExprProfile: names for all sample-E samples
sampleNameFileX - Variable in class ProtPlot: Name of the current sample Name File X
sampleNameFileY - Variable in class ProtPlot: Name of the current sample Name File Y
sampleNbr - Variable in class ReadPRP: The sampleNbr for the sample being read
sampleX - Variable in class ProtPlot: current index of the ReadPRP PRP database (X/Y) ratio sample X
sampleXlist - Variable in class ProtPlot: boolean list of samples used in the X set [0:nPRPs-1]
sampleY - Variable in class ProtPlot: current index of the ReadPRP PRP database (X/Y) ratio sample Y
sampleYlist - Variable in class ProtPlot: list of samples used in the Y set [0:nPRPs-1]
saName - Static variable in class ProtPlot: [0:nSAparam-1] name
saValue - Static variable in class ProtPlot: [0:nSAparam-1] value
saveAsButton - Variable in class ShowStringPopup: "SaveAs" .txt button
saveAsGIF - Variable in class ExprProfilePopup: Save display as GIF file
saveCluster() - Method in class Cluster: saveCluster() - save current clustered proteins into prp.savedClusterMPIDs[]
savedClusterMPIDs - Variable in class ProtPlot: List [0:nSavedClusterMPIDs-1] of mPids of saved clustered proteins
savedClusterMPIDsMap - Variable in class ProtPlot: boolean map of saved clustered MPIDs
savedClusterNbrMPIDs - Variable in class ProtPlot: List [0:nSavedClusterMPIDs-1] of cluster numberssy of saved clustered proteins
savedClusterSeedSP_ACC - Variable in class ProtPlot: saved cluster SP-ACC
savedFilterMPIDs - Variable in class ProtPlot: List [0:nSavedFilterMPIDs-1] of mPids of saved Filtered proteins
savedFilterMPIDsMap - Variable in class ProtPlot: boolean map of saved clustered MPIDs
savedMsg - Variable in class ShowStringPopup: message after Saved Txt into file
saveFilter() - Method in class Filter: saveFilter() - save current Filtered proteins into prp.savedFilterMPIDs[]
saveNamedProteinSet(String, String) - Method in class UtilPRP: saveNamedProteinSet() - save the named protein set as a "Set/*.set" file.
saveProteinSetFile(String) - Method in class ShowScatterPlotPopup: saveProteinSetFile() - open a new protein set database file.
saveSamplesList() - Method in class PopupPRPlistSelector: saveSamplesList() - Save the save list back into the PRP DB
saveScatterPlotAsGIF() - Method in class ShowScatterPlotPopup: saveScatterPlotAsGIF() - save the scatterplot as a GIF image file in Report
sbSize - Variable in class ExprProfileScrollPane: width of scroll bar control
scale - Variable in class Draw2DprotPlot
SCALE_DEF - Static variable in class Draw2DprotPlot
scaleX - Variable in class Draw2DprotPlot
scaleXplot - Variable in class Draw2DprotPlot
scaleY - Variable in class Draw2DprotPlot
scaleYplot - Variable in class Draw2DprotPlot
scrHeight - Variable in class ProtPlot: screen size height
scrWidth - Variable in class ProtPlot: screen size width
sdX - Static variable in class MathPRP: RTN: standard deviation X
sdY - Static variable in class MathPRP: RTN: standard deviation Y
SEL_CUR_SAMPLE - Static variable in class PopupPRPlistSelector: Select current sample
SEL_CUR_SAMPLE - Static variable in class ShowScatterPlotPopup: Select current sample
SEL_EP_SAMPLES - Static variable in class PopupPRPlistSelector: Select EP sample
SEL_EP_SAMPLES - Static variable in class ShowScatterPlotPopup: Select current sample
SEL_X_SAMPLE - Static variable in class PopupPRPlistSelector: Select Y sample or sample set
SEL_X_SAMPLE - Static variable in class ShowScatterPlotPopup: Select current sample
SEL_Y_SAMPLE - Static variable in class PopupPRPlistSelector: Select Y sample or sample set
SEL_Y_SAMPLE - Static variable in class ShowScatterPlotPopup: Select current sample
selSample - Variable in class PopupPRPlistSelector: new selected sample if not -1
selType - Variable in class PopupPRPlistSelector
sepp - Variable in class ExprProfileScrollPane: Parent window
set2DplotSubtitles(String, String, String, String, String, String) - Method in class Draw2DprotPlot: set2DplotSubtitles() - set info1,2,3,4,5,6 subtitles for plot
setAllButton - Variable in class PopupPRPlistSelector: "Set all" window button
setAllParamDefaults() - Method in class ProtPlot: setAllParamDefaults() - reset all parameter defaults using the built in values if can not find the parameter in the prp.stateFile file
setCancerButton - Variable in class PopupPRPlistSelector: "Set 'cancer'" window button
setClusterMethod(int) - Static method in class Cluster: setClusterMethod() - set method to use for clustering
setCurProtein(int) - Method in class ExprProfileScrollPane: setCurProtein() - set current protein if mPid is not -1
setCurProtein(int, boolean) - Method in class DrawProtScatterPlot: setCurProtein() - set current protein spot to mPid if it exists (not -1).
setDefaultXYEPsets(String, String, String) - Method in class ProtPlot: setDefaultXYEPsets() - set the default X, Y, EP sample sets by keywords If the keyword is null, then do not set the set.
setDistMode(int) - Static method in class Cluster: setDistMode() - set the method to use for clustering
setDistThreshold(float) - Static method in class Cluster: setDistThreshold() - set the distance threshold to use for clustering
setEPcanvasDrawingOptions(int, int) - Method in class ExprProfileScrollPane: setEPcanvasDrawingOptions() - set err-bar & zoom status and then repaint.
setFilterProtSetDiffFromFiles() - Method in class ShowScatterPlotPopup
setFilterProtSetIntersectFromFiles() - Method in class ShowScatterPlotPopup
setFilterProtSetUnionFromFiles() - Method in class ShowScatterPlotPopup
setGroupButtonsEnable(boolean) - Method in class PopupPRPlistSelector: setGroupButtonsEnable() - set the enable state of the sample assignement buttons: "Set all", "Clear all", "Set normal", "Set precancer", "Set cancer"
setNewDraw2DprotPlot() - Method in class DrawProtScatterPlot: setNewDraw2DprotPlot() - reset data structures for new sample
setNormalButton - Variable in class PopupPRPlistSelector: "Set 'normal'" window button
setPlotModeName() - Method in class UtilPRP: setPlotModeName() - lookup the plot mode name
setPlotModeState(CheckboxMenuItem) - Method in class ShowScatterPlotPopup
setPrecancerButton - Variable in class PopupPRPlistSelector: "Set 'precancer'" window button
setProteinsPerSampleScodeLabels() - Method in class PopupPRPlistSelector: setProteinsPerSampleScodeLabels() - set the Scode for all checkbox labels.
setSamplesListsFromState() - Method in class ProtPlot: setSamplesListsFromState() - read the sample lists from the state data has already been read int hash table
setScrollBarPos(int) - Method in class ExprProfileScrollPane: setScrollBarPos() - set the scroll barPosition for this panel.
setScrollerStateLabelValues() - Method in class ShowScatterPlotPopup: setScrollerStateLabelValues() - set scroller labels to the current state prp.xxxxUB/LB
setScrollersToState() - Method in class ShowScatterPlotPopup: setScrollersToState() - reset the scrollers to the current state prp.xxxxUB/LB.
setSliderStateEnabled() - Method in class ShowScatterPlotPopup: setSliderStateEnabled() - set the slide enables based on the state [BUG] does not gray out - instead it removes the cursor - not good GUI design
setStatusAreaVisible(boolean) - Method in class ProtPlot: setStatusAreaVisible() - show or hide three status lines in status popup
setStatusWindowVisible(boolean) - Method in class PopupStatusWindow: setStatusWindowVisible() - hide the window
setText1(String) - Method in class UtilPRP: setText1() - change the text1 msg for the panel.
setText1(String, Color, Color) - Method in class UtilPRP: setText1() - change the text1 field in the panel with fg, bg colors You can save the msg as the title.
setText2(String) - Method in class UtilPRP: setText2() - change the text2 field in the panel.
setText2(String, Color, Color) - Method in class UtilPRP: setText2() - change the text2 field in the panel with fg, bg colors
setText3(String) - Method in class UtilPRP: setText3() - change the text3 field in the panel.
setText3(String, Color, Color) - Method in class UtilPRP: setText3() - change the text3 field in the panel with fg, bg colors
setText4(String) - Method in class UtilPRP: setText4() - change the text4 field in the panel.
setText4(String, Color, Color) - Method in class UtilPRP: setText4() - change the text4 field in the panel with fg, bg colors
setupArrays(int) - Method in class Draw2DprotPlot: setupArrays() - setup the arrays.
setupData(int) - Method in class ExprProfile: setupData() - setup the data arrays for the other computations
setupLocalEPsetData(int, boolean) - Method in class Filter: setupLocalEPsetData() - setup local EP sets data arrays for pM
setupLocalXYsetData(int, boolean) - Method in class Filter: setupLocalXYsetData() - setup local X, and Y sets data arrays for pM
setupXYlabels() - Method in class Filter: setupXYlabels() - set the XY labels based on samples selected.
showAllXYproteinsIfNullSamplesFlag - Variable in class ProtPlot: "Show all X and Y samples if doing X/Y filtering [CB]" checkbox
showAssocWebPageFlag - Variable in class DrawProtScatterPlot: flag to allow popup web access to associated protein database
showClusteredProteinsFlag - Variable in class ProtPlot: "Show clustered proteins by black boxes [CB] flag
showErrBarsCheckBox - Variable in class ExprProfilePopup: checkbox to show error bars
showExprProfilesFilteredReport() - Method in class ReportPRP: showExprProfilesFilteredReport() - show popup of expression profiles of filtered proteins
ShowExprProfilesPopup - class ShowExprProfilesPopup.: The class pops up a window to display a list of expression profiles for the data filtered genes.
ShowExprProfilesPopup(ProtPlot, int[], int, String, boolean) - Constructor for class ShowExprProfilesPopup: ShowExprProfilesPopup() - Constructor.
showFeatures(String, String) - Method in class UtilPRP: showFeatures() - print features to txtField2 and txtField3
showFilteredLinesFlag - Variable in class ShowExprProfilesPopup
showFilteredReport() - Method in class ReportPRP: showFilteredReport() - show popup report of filtered proteins in the prp.mPidFiltered[0:prp.nMpidFiltered-1] list of mPids [TODO] Sort by expression or by ratioX/Y
showListOfExprProfileSamplesReport() - Method in class ReportPRP: showListOfExprProfileSamplesReport() - show popup report of list of samples in the current Protein expression profile.
showMsg(String) - Method in class UtilPRP: showMsg() - print msg to showStatus() and to txtField1
showMsg(String, Color, Color) - Method in class UtilPRP: showMsg() - print msg to showStatus() and to txtField1
showMsg1(String, Color, Color) - Method in class UtilPRP: showMsg1() - print msg to showStatus() and to txtField1 and change color
showMsg2(String) - Method in class UtilPRP: showMsg2() - print msg2 to txtField2
showMsg2(String, Color, Color) - Method in class UtilPRP: showMsg2() - print msg2 to txtField2 and change color
showMsg3(String) - Method in class UtilPRP: showMsg3() - print msg3 to txtField3
showMsg3(String, Color, Color) - Method in class UtilPRP: showMsg3() - print msg3 to txtField3 ALSO: side effect of setting cursor to WAIT_CURSOR if the (fg,bg) is not (black,white).
showMsg4(String) - Method in class UtilPRP: showMsg4() - print msg2 to txtField4
showMsg4(String, Color, Color) - Method in class UtilPRP: showMsg4() - print msg4 to txtField4 ALSO: side effect of setting cursor to WAIT_CURSOR if the (fg,bg) is not (black,white).
showProteinOfInterest(int, int, boolean) - Method in class DrawProtScatterPlot: showProteinOfInterest() - show quant&NCBI data if click on a point in plot
showSampleAssignmentsReport() - Method in class ReportPRP: showSampleAssignmentsReport() - list sample assignments in various sets
showSampleNbrsReport() - Method in class ReportPRP: showSampleNbrsReport() - list the samples and numbers of proteins/sample
ShowScatterPlotPopup - class ShowScatterPlotPopup.: Class ShowScatterPlotPopup.java - main popup window containing a scatterplot, pull-down menu, scatterplot scrollers, expression range scrollers, cluster distance scroller, checkboxes, etc as part of the GUI.
ShowScatterPlotPopup(ProtPlot, String) - Constructor for class ShowScatterPlotPopup: ShowScatterPlotPopup() - constructor
showSimilarProteinReport(Cluster) - Method in class ReportPRP: showSimilarProteinReport() - show popup similar-cluster report of similar proteins that were previously clustered.
showStateReport() - Method in class ReportPRP: showStateReport() - show popup of the state values including slider values
ShowStringPopup - class ShowStringPopup.: The ShowStringPopup class creates and displays scrollable string text area in a popup window.
ShowStringPopup(ProtPlot, String, String, int, int, String, String, int) - Constructor for class ShowStringPopup: ShowStringPopup() - Constructor.
showWebPageFlag - Variable in class ProtPlot: Allow access to Web if click on spot
showXYEPsetsMissingProtFilteredReport() - Method in class ReportPRP: showXYEPsetsMissingProtFilteredReport() - show popup of X&Y or EP sets statistics of missing prot filtered proteins
shrinkCube(MC_Cube) - Method in class MedianCut: shrinkCube() - Encloses "cube" with a tight-fitting cube by updating the (rmin,gmin,bmin) and (rmax,gmax,bmax) members of "cube".
simClustTitle - Variable in class Cluster: title for current similar cluster string
similarProteinsReportStr() - Method in class Cluster: similarProteinsReportStr() - compute report string of similar-cluster of filtered proteins
similarRptPopup - Variable in class Cluster: the instance of the cluster report.
sleepFlag - Variable in class PopupDialogQuery: wait for button to be pushed
sleepMsec(int) - Static method in class UtilPRP: sleepMsec() - sleep nMsec where nMsec must be >= 0 milliseconds.
sMaxX - Variable in class Draw2DprotPlot
sMaxY - Variable in class Draw2DprotPlot
sMinX - Variable in class Draw2DprotPlot
sMinY - Variable in class Draw2DprotPlot
sortAssendingFlag - Variable in class ProtPlot: "Sort report assending order[CB]"
sortedIdxToNamesIdx - Variable in class PopupFamilyNameSelector: map table to map sorted index to name idx
sortedIdxToNamesIdx - Variable in class PopupTissueNameSelector: map table to map sorted index to name idx
sortedNamesIdx - Variable in class PopupFamilyNameSelector: index list of names sorted alphabetically by familyNames[]
sortedNamesIdx - Variable in class PopupTissueNameSelector: index list of names sorted alphabetically by tissueNames[0:nTissues-1]
spaces - Variable in class PopupDialogQuery: DEF_COL_SIZE spaces
sPanel - Variable in class ShowScatterPlotPopup: panel which holds scrollable canvas
spp - Variable in class Draw2DprotPlot: instance of ShowScatterPlotPopup if the parent, else null
spp - Variable in class DrawProtScatterPlot: instance of ShowScatterPlotPopup
spp - Variable in class EventHandlerPRP: Instance of ShowScatterPlotPopup
spp - Variable in class PopupFamilyNameSelector
spp - Static variable in class PopupPRPlistSelector
spp - Variable in class PopupTissueNameSelector
spp - Variable in class ProtPlot: main window containing the 2D plot and menu bar
spp - Variable in class ShowStringPopup: link to instance
spp - Static variable in class UtilPRP: instance of ShowScatterPlotPopup
startPopupDialog(String, int) - Method in class PopupDialogQuery: startPopupDialog() - create a hidden dialog panel within a frame.
stat - Variable in class Filter: instance of StatisticsPRP
stat - Variable in class ProtPlot: statistics package
stat - Variable in class ReportPRP: Instance of StatisticsPRP.
stateFile - Static variable in class ProtPlot: Current state file.
stateName - Static variable in class ProtPlot: Current state name is the stateFile without the ".prpstate"
StatisticsPRP - class StatisticsPRP.: The class contains various parametric and non-parametric probability statistics methods used in computing statistics for ProtPlot.
StatisticsPRP(ProtPlot) - Constructor for class StatisticsPRP: StatisticsPRP() - constructor
statusAreaIsVisibleFlag - Variable in class ProtPlot: The 3 Status lines area visibility flag.
statusCheckBox - Variable in class ShowScatterPlotPopup: HideStatus/ShowStatus selection
statusPopup - Variable in class ProtPlot: Holds the popup window status lines
stdDevEPdata - Variable in class Filter: computed std deviation EP set data for current protein
stdDevExpr - Variable in class ExprProfile: StdDev of expression of the sampleData[] values.
stdDevH - Variable in class StatisticsPRP: standard deviation of data[]
stdDevXdata - Variable in class Filter: computed std deviation X set data for current protein
stdDevYdata - Variable in class Filter: computed std deviation Y set data for current protein
strictDataFormatFlag - Variable in class ReadPRP: Flag determines whether strict parsing is used.
SWISS2D_BASEURL - Static variable in class ProtPlot: Hardwired URLs and file names
swissProtAcc - Variable in class Protein: SwissProt Acc (accession number)
swissProtId - Variable in class Protein: SwissProt ID (name of the protein)
swissProtServerBase - Variable in class ProtPlot: swiss prot server

T

t - Variable in class StatisticsPRP: CALC: t or t' statistic
TARGET_SIZE - Static variable in class Draw2DprotPlot
TARGET_SIZE - Static variable in class ExprProfileCanvas: target Size for selecting a line
test_XYsets_KS_Test(int, float, boolean) - Method in class Filter: test_XYsets_KS_Test() - test if X and Y sets pass Kolmogorov-Smirnov Test with a pValue better than pValueThr.
test_XYsets_t_Test(int, float, boolean) - Method in class Filter: test_XYsets_t_Test() - test if X and Y sets pass the t-Test with a pValue better than pValueThr.
textarea - Variable in class ShowStringPopup: Text area GUI for main report
textField - Variable in class PopupDialogQuery: place text to be edited here
textFontFamily - Variable in class ProtPlot: default text font family name
textReport - Variable in class ShowStringPopup: copy of text in textArea
thresholdNsamples - Variable in class ProtPlot: Number of samples threshold slider
thresholdSproteins - Variable in class ProtPlot: Number of proteins/sample (S) threshold slider
TISSUE_NAMES_FILE - Static variable in class ProtPlot: Name of file with tab-delim list of tissues (name, bits)
tissueANDCheckBox - Variable in class PopupTissueNameSelector
tissueBits - Variable in class PopupTissueNameSelector: list of tissue bits
tissueBits - Variable in class Protein: bits corresponding to tissueList[] names
tissueBits - Variable in class ReadTissues: list of tissue tissue BITS [0:nFamilies-1] return all tokens/row the tissueBit[i] = 2**tissueNbr[i].
tissueNameCheckbox - Variable in class PopupTissueNameSelector
tissueNameFrame - Variable in class PopupTissueNameSelector
tissueNames - Variable in class PopupTissueNameSelector: list of tissue names
tissueNames - Variable in class ReadTissues: List of tissue names [0:nTissues-1] return all tokens/row
tissueNamesFile - Variable in class ProtPlot: tissue name file
tissueNamesFile - Variable in class ReadTissues: Name of the tissue data tab-delimited file.
tissueNbrs - Variable in class ReadTissues: list of tissue tissue Numbers [0:nFamilies-1] return all tokens/row
title - Variable in class Draw2DprotPlot
title - Variable in class ExprProfileCanvas: ARG: opt.
title - Variable in class ExprProfileScrollPane: title for entire EP.
title - Variable in class ShowExprProfilesPopup: ARG: for PopupRegistry
title - Variable in class ShowScatterPlotPopup: ARG: title of popup plot
title - Variable in class ShowStringPopup: string for title of frame
title - Variable in class StatisticsPRP: for data used in histogram
titleFont - Variable in class Draw2DprotPlot: The title font
titleFont - Static variable in class ExprProfileCanvas
titleLabel - Variable in class ShowScatterPlotPopup: title for the main window
TMAP_JAR_VERSION_FILE - Static variable in class ProtPlot: name of file containing the latest ProtPlot.jar version #
tokArray - Variable in class ReadPRP: token parse array [0:nCols-1] return all tokens/row
tokBuf - Variable in class ReadFamilies: token buffer
tokBuf - Variable in class ReadPRP: token buffer for parsing a line
tokBuf - Variable in class ReadTissues: token buffer
topTitle1 - Variable in class Draw2DprotPlot
topTitle2 - Variable in class Draw2DprotPlot
topTitle3 - Variable in class Draw2DprotPlot
topTitle4 - Variable in class Draw2DprotPlot
toString() - Method in class Protein: toString() - prettyprint Protein data
TOTAL_PRP_EXTENSION - Static variable in class ProtPlot: Only read PRP files with this file extension.
txtField1 - Variable in class PopupStatusWindow
txtField2 - Variable in class PopupStatusWindow
txtField3 - Variable in class PopupStatusWindow
txtField4 - Variable in class PopupStatusWindow

U

UNDER_DALTON_LIMIT - Static variable in class ProtPlot: default bound for toggling data base between xxx_tot.prp and the subset <= this limit.
up - Variable in class MC_Cube
update2Dplot(String, String, String, String, String, String, String, String, String, String, int, int, double, double, double, double, double, double) - Method in class Draw2DprotPlot: update2Dplot() - set data for plot.
updateCurProtein(int) - Method in class ExprProfileScrollPane: updateCurProtein()- update the current protein in the EP plot list.
updateCurProtein(int) - Method in class ShowExprProfilesPopup: updateCurProtein() - update expression profile plot list if current protein changed and this type of string report requires it.
updateCurProtein(int) - Method in class ShowScatterPlotPopup: updateCurProtein() - update plot if current protein changed and this type of plot requires it.
updateData(int) - Method in class ExprProfile: updateData() - update expression profile with new gene data
updateData(int[], int, String) - Method in class ExprProfileScrollPane: updateData() - update expression profile scroller with new protein data.
updateData(int, String, boolean) - Method in class ExprProfileCanvas: updateData() - update expression profile plot with new protein data.
updateData(int, String, boolean) - Method in class ExprProfilePanel: updateData() - update expression profile with new protein data if a legal protein mPid.
updateData(int, String, boolean) - Method in class ExprProfilePopup: updateData() - update expression profile with new protein data.
updateEPplots(int[], int) - Method in class ShowExprProfilesPopup: updateEPplots() - update expression profile plots using new GeneList.
updateEPtitles() - Method in class ExprProfileScrollPane: updateEPtitles() - generate array of titles for drawing in expression profile plots
updateFilter(int[], int, String) - Method in class ShowExprProfilesPopup: updateFilter() - update expression profile plots using new protein list.
updateLabels() - Method in class ShowExprProfilesPopup: updateLabels() - update string report if labels changed and this type of plot requires it.
updatePlot() - Method in class ShowScatterPlotPopup: updatePlot() - update the popup plot
updatePopupDialog(String, String, String[], int) - Method in class PopupDialogQuery: updatePopupDialog() - display/unhide popup dialog frame and set new values.
updateProtPlotJarFile() - Method in class UtilPRP: updateProtPlotJarFile() - update ProtPlot.jar into program install area.
updateProtPlotProgram() - Method in class UtilPRP: updateProtPlotProgram() - verify that want to update the ProtPlot.jar file from the maexplorer.sourceforge.net server.
updateProtPlotPRPdatabase() - Method in class UtilPRP: updateProtPlotPRPdatabase() - verify that want to update PRP/*.prp files from the current server.
updateProtPlotPRPfile(int, String) - Method in class UtilPRP: updateProtPlotPRPfile() - update ProtPlot PRP/*.prp files into PRP/ install area.
updateReport() - Method in class ReportPRP: updateReport() - update the popup report if possible using the rptType.
updateScaling(boolean) - Method in class Draw2DprotPlot: updateScaling() - set scaling mode in proper sub-object.
updateScatterPlot() - Method in class DrawProtScatterPlot: updateScatterPlot() - refresh scatterplot data and redraw the canvas
updateScatterPlot(String) - Method in class ShowScatterPlotPopup: updateScatterPlot() - create a 2D gel popup scatterplot from raw data.
updateScrolledRegion(float, float, float, float) - Method in class Draw2DprotPlot: updateScrolledRegion() - update scrolled region to plot [(x1,y1):(x2,y2)].
updateSeedProtein(int) - Static method in class Cluster: updateSeedProtein() - update the seed protein mPid used for clustering and recluster if enabled
updateSimilarProteinsReport() - Method in class Cluster: updateSimilarProteinsReport() - compute report string of similar-cluster of filtered proteins [TODO] This will update the Cluster Report window text area.
updateSlider() - Method in class ShowExprProfilesPopup: updateSlider() - update expression profile plot list if Slider changed
updateSlider() - Method in class ShowScatterPlotPopup: updateSlider() - update plot if Slider changed and this type of plot requires it.
updateText(String, String) - Method in class ShowStringPopup: updateText() - update text in popup window
USE_FAMILIES_FILE_FLAG - Static variable in class ProtPlot: Set if read protein Family data from FAMILY_NAMES_FILE
USE_LINEAR_SCROLLING - Static variable in class ProtPlot: use linear else non-linear scroller scaling
useCmapRatioModeFlag - Variable in class ProtPlot: plot samplesX/sampleY ratio range color map in the scatterplot
useDichromasyFlag - Variable in class ProtPlot: color blind filter
useEPsetExprModeFlag - Variable in class ProtPlot: Show mean EP set sample expression
useExponentialMapFlag - Variable in class ProtPlot: If enabled, it generates a non-linear colormap using the eMap[gray] function to generate a 10 color eColor[0:9] set of colors stored in cMap[0:155].
useExprFlag - Variable in class ProtPlot: "Expression/Location" checkbox
useExprModeFlag - Variable in class ProtPlot: plot the current sample expression data in the scatterplot
useExprProfilePlotModeFlag - Variable in class ProtPlot: if true, then popup expression profile in epp
useFamilyANDflag - Variable in class ProtPlot: use AND else OR of Family filters
useFamilyBits - Variable in class ProtPlot: selected current protein family bits
useFamilyFilterFlag - Variable in class ProtPlot: enable gene Family name filtering
useFilterByXY_KStestFlag - Variable in class ProtPlot: "Filter by X & Y sets Kolmogorov-Smirnov test results [RB]"
useFilterByXYsetMissingProteinsFlag - Variable in class ProtPlot: "Filter by X & Y sets missing proteins [CB]"
useFilterByXYtTestFlag - Variable in class ProtPlot: "Filter by X & Y sets t-test results [RB]"
useFilterExprRangeFlag - Variable in class ProtPlot: "Filter by Expression range" checkbox filters
useFiltersFlag - Variable in class ProtPlot: "Filter/NoFilter" checkbox for ANY active filters
useGenBankFlag - Variable in class ProtPlot: GenBank Web access
useHomeServer - Static variable in class ProtPlot: ProtPlot home server to use
useInitialStateFileFlag - Static variable in class ProtPlot: Only read initial state file if this is set
useLocalDocFlag - Variable in class ProtPlot: Flag to use local Doc/ directory for help else to use ProtPlot server
useMouseOverFlag - Variable in class ProtPlot: "useMouseOver" for popup tracking balloons
useProClassFlag - Variable in class ProtPlot: access ProClass if click on spot
usePRPlistFilterFlag - Variable in class ProtPlot: enable gene PRP list name filtering
usePseudocolorFlag - Variable in class ProtPlot: "Use pseudocolor else grayscale for expression, checkbox
useRatioModeFlag - Variable in class ProtPlot: Show ratio X/Y or X-set/Y-set, else single sample expression or mean EP set expression
userDir - Static variable in class ProtPlot: user directory where project was started.
useRGratioModeFlag - Variable in class ProtPlot: plot samplesX/sampleY ratio (Red=X + Green=Y) data in the scatterplot
useSavedClusterFlag - Variable in class ProtPlot: Use saved clustered set of proteins in data filter
useSavedFilterFlag - Variable in class ProtPlot: Use saved filtered set of proteins in data filter
useSingleExprModeFlag - Variable in class ProtPlot: Show single sample expression
useSwissProtFlag - Variable in class ProtPlot: access SwissProt if click on spot
useTest - Variable in class StatisticsPRP: CALC: 'B' or 'T' - t-test to use
useTissueANDflag - Variable in class ProtPlot: use AND else OR of tissue filters
useTissueBits - Variable in class ProtPlot: selected current tissues bits
useTissueFilterFlag - Variable in class ProtPlot: enable Tissue name filtering
useTotPRPflag - Variable in class ProtPlot: if true, access all proteins, otherwise filter out all proteins > UNDER_DALTON_LIMIT Daltons.
useVariableRadiusFlag - Variable in class ProtPlot: use variable radius for drawing spots proportional to the expression else all the same size
useXYsetCheckBox - Variable in class ShowScatterPlotPopup
useXYsetCmapRatioModeFlag - Variable in class ProtPlot: plot X-Set-samples /X-Set-samples ratio range color map scatterplot
useXYsetDataFlag - Variable in class ProtPlot: use X / Y sets of samples else use single X / Y samples
util - Static variable in class Cluster: Utility instance
util - Variable in class Draw2DprotPlot: instance of UtilPRP
util - Variable in class DrawProtScatterPlot: instance of UtilPRP
util - Variable in class EventHandlerPRP: instance of UtilPRP
util - Variable in class ExprProfileCanvas: instance of UtilPRP
util - Variable in class ExprProfileScrollPane
util - Variable in class FileIOPRP: instance of UtilPRP
util - Variable in class Filter: instance of UtilPRP
util - Variable in class GetListOfPRPs: instance of UtilPRP
util - Static variable in class MathPRP: instance of UtilPRP
util - Variable in class ProtPlot: Utility instance
util - Variable in class ReadFamilies: instance of UtilPRP
util - Variable in class ReadPRP: instance of UtilPRP
util - Variable in class ReadTissues: instance of UtilPRP
util - Variable in class ReportPRP: Utility instance
util - Variable in class ShowExprProfilesPopup: link to global instance
util - Variable in class ShowScatterPlotPopup: instance of UtilPRP
util - Static variable in class StatisticsPRP: instance of UtilPRP
UtilPRP - class UtilPRP.: Class UtilPRP contains common utility fcts.
UtilPRP(ProtPlot) - Constructor for class UtilPRP: Util() - constructor

V

VERSION - Static variable in class ProtPlot
versionStateFile - Variable in class ProtPlot: Version of the read from stateFile ".prpstate" if not null
verStr - Static variable in class ProtPlot
vertCaption - Variable in class Draw2DprotPlot
vertLBscr - Variable in class ShowScatterPlotPopup: vertical (top,bottom) scrollers for the for canvas
vertUBscr - Variable in class ShowScatterPlotPopup: vertical (top,bottom) scrollers for the for canvas
viewClusterBoxesCheckBox - Variable in class ShowStringPopup: toggle black boxes on clustered proteins in scatterplot
VISIBLE_SCR - Static variable in class ShowScatterPlotPopup: scrollbar's visible amount
vs - Variable in class ExprProfileScrollPane: vertical scroll bar
vsValLB - Variable in class ProtPlot: (pI) Vertical slider initial value Lower Bound
vsValUB - Variable in class ProtPlot: (pI) Vertical slider initial value Upper Bound

W

width - Variable in class PopupDialogQuery: size of frame
width - Variable in class WriteGifEncoder
width - Variable in class MedianCut: width size of image
Width - Variable in class WriteGifEncoder
windowActivated(WindowEvent) - Method in class ExprProfilePopup
windowActivated(WindowEvent) - Method in class PopupDialog
windowActivated(WindowEvent) - Method in class PopupDialogQuery
windowActivated(WindowEvent) - Method in class PopupFamilyNameSelector
windowActivated(WindowEvent) - Method in class PopupPRPlistSelector
windowActivated(WindowEvent) - Method in class PopupStatusWindow
windowActivated(WindowEvent) - Method in class PopupTissueNameSelector
windowActivated(WindowEvent) - Method in class ShowExprProfilesPopup
windowActivated(WindowEvent) - Method in class ShowScatterPlotPopup
windowActivated(WindowEvent) - Method in class ShowStringPopup
windowClosed(WindowEvent) - Method in class ExprProfilePopup
windowClosed(WindowEvent) - Method in class PopupDialog
windowClosed(WindowEvent) - Method in class PopupDialogQuery
windowClosed(WindowEvent) - Method in class PopupFamilyNameSelector
windowClosed(WindowEvent) - Method in class PopupPRPlistSelector
windowClosed(WindowEvent) - Method in class PopupStatusWindow
windowClosed(WindowEvent) - Method in class PopupTissueNameSelector
windowClosed(WindowEvent) - Method in class ShowExprProfilesPopup
windowClosed(WindowEvent) - Method in class ShowScatterPlotPopup
windowClosed(WindowEvent) - Method in class ShowStringPopup
windowClosing(WindowEvent) - Method in class ExprProfilePopup: windowClosing() - closing down the window, get rid of the frame.
windowClosing(WindowEvent) - Method in class PopupDialog: windowClosing() - close down the window on PC only.
windowClosing(WindowEvent) - Method in class PopupDialogQuery: windowClosing() - close down the window on PC only.
windowClosing(WindowEvent) - Method in class PopupFamilyNameSelector: windowClosing() - close down the window.
windowClosing(WindowEvent) - Method in class PopupPRPlistSelector: windowClosing() - close down the window.
windowClosing(WindowEvent) - Method in class PopupStatusWindow: windowClosing() - hide the window.
windowClosing(WindowEvent) - Method in class PopupTissueNameSelector: windowClosing() - close down the window.
windowClosing(WindowEvent) - Method in class ShowExprProfilesPopup: windowClosing() - closing down the window, get rid of the frame.
windowClosing(WindowEvent) - Method in class ShowScatterPlotPopup: windowClosing() - close down the window.
windowClosing(WindowEvent) - Method in class ShowStringPopup: windowClosing() - closing down the window, get rid of the frame.
windowDeactivated(WindowEvent) - Method in class ExprProfilePopup
windowDeactivated(WindowEvent) - Method in class PopupDialog
windowDeactivated(WindowEvent) - Method in class PopupDialogQuery
windowDeactivated(WindowEvent) - Method in class PopupFamilyNameSelector
windowDeactivated(WindowEvent) - Method in class PopupPRPlistSelector
windowDeactivated(WindowEvent) - Method in class PopupStatusWindow
windowDeactivated(WindowEvent) - Method in class PopupTissueNameSelector
windowDeactivated(WindowEvent) - Method in class ShowExprProfilesPopup
windowDeactivated(WindowEvent) - Method in class ShowScatterPlotPopup
windowDeactivated(WindowEvent) - Method in class ShowStringPopup
windowDeiconified(WindowEvent) - Method in class ExprProfilePopup
windowDeiconified(WindowEvent) - Method in class PopupDialog
windowDeiconified(WindowEvent) - Method in class PopupDialogQuery
windowDeiconified(WindowEvent) - Method in class PopupFamilyNameSelector
windowDeiconified(WindowEvent) - Method in class PopupPRPlistSelector
windowDeiconified(WindowEvent) - Method in class PopupStatusWindow
windowDeiconified(WindowEvent) - Method in class PopupTissueNameSelector
windowDeiconified(WindowEvent) - Method in class ShowExprProfilesPopup
windowDeiconified(WindowEvent) - Method in class ShowScatterPlotPopup
windowDeiconified(WindowEvent) - Method in class ShowStringPopup
windowIconified(WindowEvent) - Method in class ExprProfilePopup
windowIconified(WindowEvent) - Method in class PopupDialog
windowIconified(WindowEvent) - Method in class PopupDialogQuery
windowIconified(WindowEvent) - Method in class PopupFamilyNameSelector
windowIconified(WindowEvent) - Method in class PopupPRPlistSelector
windowIconified(WindowEvent) - Method in class PopupStatusWindow
windowIconified(WindowEvent) - Method in class PopupTissueNameSelector
windowIconified(WindowEvent) - Method in class ShowExprProfilesPopup
windowIconified(WindowEvent) - Method in class ShowScatterPlotPopup
windowIconified(WindowEvent) - Method in class ShowStringPopup
windowOpened(WindowEvent) - Method in class ExprProfilePopup
windowOpened(WindowEvent) - Method in class PopupDialog
windowOpened(WindowEvent) - Method in class PopupDialogQuery
windowOpened(WindowEvent) - Method in class PopupFamilyNameSelector
windowOpened(WindowEvent) - Method in class PopupPRPlistSelector
windowOpened(WindowEvent) - Method in class PopupStatusWindow
windowOpened(WindowEvent) - Method in class PopupTissueNameSelector
windowOpened(WindowEvent) - Method in class ShowExprProfilesPopup
windowOpened(WindowEvent) - Method in class ShowScatterPlotPopup
windowOpened(WindowEvent) - Method in class ShowStringPopup
writeFile(String) - Method in class WriteGifEncoder: writeFile() - write the Gif encoded image to output file
writeFileToDisk(String, String) - Method in class FileIOPRP: writeFileToDisk() - write string data to a local disk file.
writeGif(FileOutputStream) - Method in class WriteGifEncoder: writeGif() - Saves the image as a GIF file.
WriteGifEncoder - class WriteGifEncoder.: The WriteGifEncoder class writes out an Image object as a named GIF file.
WriteGifEncoder(Image) - Constructor for class WriteGifEncoder: WriteGifEncoder() - Constructs using 24-bit Image.
WriteGifEncoder(int, int, byte[], byte[], byte[], byte[]) - Constructor for class WriteGifEncoder: WriteGifEncoder() - Constructs a new WriteGifEncoder.
WriteGifEncoderHashitem - class WriteGifEncoderHashitem.
WriteGifEncoderHashitem(int, int, int, boolean) - Constructor for class WriteGifEncoderHashitem: WriteGifEncoderHashitem() - constructor
writeState(String) - Method in class UtilPRP: writeState() - write the ProtPlot State into stateFile in the same directory that the project is in.
writeString(FileOutputStream, String) - Static method in class WriteGifEncoder: writeString() - write string to the file.

X

xBase - Variable in class Draw2DprotPlot: baseline for xList to xPnt
xCondLabel - Variable in class ProtPlot: plot label: (className,mnData,sdData,cvData) X (set) for current protein if previously called the t-test
xCondName - Variable in class ProtPlot: condition name for all X set members
xCoord - Variable in class ExprProfile: X coords for all sample vert lines in canvas for event handler...
xcurProtein - Variable in class Draw2DprotPlot: current protein if defined
xCursor - Variable in class ExprProfileCanvas: event handler mouse X cursor coordinates
xData - Variable in class Filter: quant data for all X (set) members.
xDataP1 - Variable in class Filter: quant data for all X (set) members.
xDataScatterPlot - Variable in class Draw2DprotPlot: X Coords [0:nPointsMax-1] used for computing ratios when clicking
xLeft - Variable in class Draw2DprotPlot
xList - Variable in class ExprProfileScrollPane: [nProteins*nHP_E] EP overlay coords
xOffset - Variable in class Draw2DprotPlot
XOFFSET_DEF - Static variable in class Draw2DprotPlot
xPlotted - Variable in class Draw2DprotPlot: X Coord [0:nPointsMax-1] for clicking on point in list
xPnt - Variable in class Draw2DprotPlot: xList[0:prp.nMpidSamples-1] data mapped to int
xRange - Variable in class Draw2DprotPlot
XRANGE_DEF - Static variable in class Draw2DprotPlot
xRight - Variable in class Draw2DprotPlot
xScale - Variable in class Draw2DprotPlot: slope for xList to xPnt
xText - Variable in class Draw2DprotPlot

Y

y1Coord - Variable in class ExprProfile: Y coord for horizontal axis for vertical line, else is label for setting current gene
yBase - Variable in class Draw2DprotPlot: baseline for yList to yPnt
yCondLabel - Variable in class ProtPlot: plot label: (className,mnData,stdData,cvData) Y (set) for current protein if previously called the t-test
yCondName - Variable in class ProtPlot: condition name for all Y set members
ycurProtein - Variable in class Draw2DprotPlot: current protein if defined
yCursor - Variable in class ExprProfileCanvas: event handler mouse Y cursor coordinates
yData - Variable in class Filter: quant data for all Y (set) members.
yDataP1 - Variable in class Filter: quant data for all Y (set) members.
yDataScatterPlot - Variable in class Draw2DprotPlot: Y Coord [0:nPointsMax-1] used for computing ratios when clicking
yList - Variable in class ExprProfileScrollPane: [nProteins*nHP_E] EP overlay coords
yOffset - Variable in class Draw2DprotPlot
YOFFSET_DEF - Static variable in class Draw2DprotPlot
yPlotted - Variable in class Draw2DprotPlot: Y Coord [0:nPointsMax-1] for clicking on point in list
yPnt - Variable in class Draw2DprotPlot: yList[0:prp.nMpidSamples-1] data mapped to int
yRange - Variable in class Draw2DprotPlot
YRANGE_DEF - Static variable in class Draw2DprotPlot
yScale - Variable in class Draw2DprotPlot: slope for yList to yPnt
yText - Variable in class Draw2DprotPlot
yTop - Variable in class Draw2DprotPlot

Z

zoomBarsButton - Variable in class ExprProfilePopup: zoom magnification button
zoomBarsButton - Variable in class ShowExprProfilesPopup
zoomBarsMag - Variable in class ExprProfileCanvas: zoom magnification: by 1X, 2X, 5X, 10X, 20X mod
zoomBarsMag - Variable in class ExprProfileScrollPane: 1X, 2X, 5X, 10X pass through to EP panel
zoomBarsMag - Variable in class ShowExprProfilesPopup: data magnification 1X, 2X, 5X, 10X, 20X

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