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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