Serialized Form
this$0
PluginUnLoader this$0
pList
PluginUnLoader.UnloaderDialog.PluginList pList
bUnload
java.awt.Button bUnload
bDone
java.awt.Button bDone
this$1
PluginUnLoader.UnloaderDialog this$1
ltList
java.awt.List ltList
rtList
java.awt.List rtList
mae
MAExplorer mae
- link to global MAExplorer instance
msR
MaHybridSample msR
- link to global MaHybridSample instance
siCanvas
ScrollableImageCanvas siCanvas
- instance of the scrollable image canvas
southPanel
java.awt.Panel southPanel
- opt. holds mae.pImage, vs & hs scroll box in SOUTH
vs
java.awt.Scrollbar vs
- opt. vertical scroll bar
hs
java.awt.Scrollbar hs
- opt. horizontal scroll bar
txtField1
java.awt.TextField txtField1
- image title placed above canvas
txtField2
java.awt.TextField txtField2
- genomic info placed above canvas
txtField3
java.awt.TextField txtField3
- additional genomic info placed above canvas
name
java.lang.String name
- HP sample name
title
java.lang.String title
- current title for window
lastFG1
java.awt.Color lastFG1
- last foreground colors cached for showMsg1
lastBG1
java.awt.Color lastBG1
- last background colors cached for showMsg1
lastFG2
java.awt.Color lastFG2
- last foreground colors cached for showMsg2
lastBG2
java.awt.Color lastBG2
- last background colors cached for showMsg2
lastFG3
java.awt.Color lastFG3
- last foreground colors cached for showMsg3
lastBG3
java.awt.Color lastBG3
- last background colors cached for showMsg3
magnification
int magnification
- magnification
preferredWidth
int preferredWidth
- width of panel
preferredHeight
int preferredHeight
- height of panel
steps
int steps
- prewired scroller steps
pagestep
int pagestep
- scrollbar thickness
img_selectedFlag
boolean img_selectedFlag
- flag: set if xObj,yObj is set
id
int id
- id # for this instance
addChangePosFlag
boolean addChangePosFlag
- if can move SELECTED entry up/down
remoteFlag
boolean remoteFlag
- true if using other prj data/ta
meh1
ChooserGUI.MouseEventHandler meh1
- handle mouse events for text areas for ta1 LEFT
meh2
ChooserGUI.MouseEventHandler meh2
- handle mouse events for text areas for ta2 RIGHT
ta1
java.awt.TextArea ta1
- REMAINDER objs
ta2
java.awt.TextArea ta2
- SELECTED obj list
addButton
java.awt.Button addButton
- mv Remainder entry to Selected
delButton
java.awt.Button delButton
- mv Selected entry to Remainder
addAllButton
java.awt.Button addAllButton
- mv ALL Remainder entries to Selected
rmvAllButton
java.awt.Button rmvAllButton
- mv ALL Selected entries to Remainder
upButton
java.awt.Button upButton
- move SELECTED entry up if possible
downButton
java.awt.Button downButton
- move SELECTED entry down if possible
controlPanel
java.awt.Panel controlPanel
- control panel for main ok/reset buttons
buttonPanel
java.awt.Panel buttonPanel
- buttons panel
prjListPanel
java.awt.Panel prjListPanel
- project prj ta
objButtonPanel
java.awt.Panel objButtonPanel
- set prj button
objListTApanel
java.awt.Panel objListTApanel
- obj list ta1
upDownPanel
java.awt.Panel upDownPanel
- panel with up/down buttons
addDelAllButtonPanel
java.awt.Panel addDelAllButtonPanel
- add,del,all buttons
selectedPanel
java.awt.Panel selectedPanel
- SELECTED list
changePosPanel
java.awt.Panel changePosPanel
- change up/down position panel
ta1Label
java.awt.Label ta1Label
- label under ta1
ta2Label
java.awt.Label ta2Label
- label under ta2
useAbove
java.awt.Label useAbove
- optional label if not to use ta1 from above
lTitle
java.awt.Label lTitle
- label for title for entire GUI window
taRows
int taRows
- rows/text area
taCols
int taCols
- columns/text area
origRemObjsSize
int origRemObjsSize
- REMAINDER list size
origSelObjsSize
int origSelObjsSize
- SELECTED list size
remObjListSize
int remObjListSize
- REMAINDER list size
selObjListSize
int selObjListSize
- SELECTED list size
title
java.lang.String title
- title for entire GUI window
taStr1
java.lang.String taStr1
- label for SELECTED LEFT text area
taStr2
java.lang.String taStr2
- label for REMAINDER RIGHT text area
origRemObjs
java.lang.String[] origRemObjs
- original REMAINDER list
origSelObjs
java.lang.String[] origSelObjs
- original SELECTED list
remObjList
java.lang.String[] remObjList
- REMAINDER list, returned if needed
selObjList
java.lang.String[] selObjList
- SELECTED list to be returned
cGUI
ChooserGUI cGUI
- This is either the remote instance or 'this' instance of ChooserGUI
for the instance of REMAINDER to use.
titleFont
java.awt.Font titleFont
- font used by title
labelFont
java.awt.Font labelFont
- font used by label
dataFont
java.awt.Font dataFont
- font used by data
cGUIpanel
java.awt.Panel cGUIpanel
- main GUI panel
parentWindow
java.lang.Object parentWindow
- parent window
preferredHeight
int preferredHeight
- preferred height size of entire canvas
preferredWidth
int preferredWidth
- preferred width size of entire canvas
statVertOffset
int statVertOffset
- offset of status canvas if drawing it at top of GIF image canvas, else 0
tree
HierClustNode tree
- hierarchical cluster tree
dcg
DrawClusterGram dcg
- parent class
objDataV
float[][] objDataV
- [0:maxGenes-1][0:nCols-1] normalized data for each object
maxDgramDist
float maxDgramDist
- max of dGramDistS[]
dGramDistS
float[] dGramDistS
- [0:nObj-2] log dist. between children
dGramDistR
float[] dGramDistR
- [0:nObj-2] log dist. between Right's children
dGramDistL
float[] dGramDistL
- [0:nObj-2] log dist. between Left's children
dGramEnumOrder
float[] dGramEnumOrder
- [0:nObj-2] enumeration order
dGramEOright
float[] dGramEOright
- [0:nObj-2] right child enum order
dGramEOleft
float[] dGramEOleft
- [0:nObj-2] left child enum order
dGramNodeNbr
int[] dGramNodeNbr
- [0:nObj-2] Node Number
dGramRightNNbr
int[] dGramRightNNbr
- [0:nObj-2] Right Node Number
dGramLeftNNbr
int[] dGramLeftNNbr
- [0:nObj-2] Left Node Number
ratioColor
java.awt.Color[] ratioColor
- used for color mapping
ratioRange
float[] ratioRange
- used for color mapping
shortWidthFlag
boolean shortWidthFlag
- flag: plot narrower boxes
addKmeansDataFlag
boolean addKmeansDataFlag
- flag: if cdg.plotMode==mae.PLOT_KMEANS_CLUSTERGRAM)
useColNbrFlag
boolean useColNbrFlag
- flag: 1, 2, 3, ... for COL name
useFullHPStageNameFlag
boolean useFullHPStageNameFlag
- flag: use full HP stage name for COL name
didDataSetupFlag
boolean didDataSetupFlag
- flag: set by setupData() if successful
foundObjFlag
boolean foundObjFlag
- found object row when clicked on it
dGramZoomMag
int dGramZoomMag
- zoom in on dendrogram - set by DrawClusterGram checkbox
font
java.awt.Font font
- drawing font
fm
java.awt.FontMetrics fm
- font metrics for font
fontHeight
int fontHeight
fontWidth
int fontWidth
fontLeading
int fontLeading
guardRows
int guardRows
- # of extra rows so cover the viewport
nRows
int nRows
- # of rows i.e. genes
nCols
int nCols
- # of columns i.e. HPs
orderedCL
GeneList orderedCL
- gene list for rows
dGramX1
int dGramX1
- left horizontal size of dendrogram region
dGramX2
int dGramX2
- right horizontal size of dendrogram region
scaleMapX
int scaleMapX
- position of scale map X
scaleMapY
int scaleMapY
- position of scale map Y
vertLabelX
int vertLabelX
- vertical label ULHC
vertLabelY1
int vertLabelY1
- top y for vert label
vertLabelY2
int vertLabelY2
- bottom y for vert label
leftLabel
int leftLabel
- left edge of Left label
leftEdge
int leftEdge
- left edge of box array
rightEdge
int rightEdge
- right edge of box array
topEdge
int topEdge
- top edge of box array
botEdge
int botEdge
boxWidth
int boxWidth
- bottom edge of box array
boxHeight
int boxHeight
- size of a data box in the clustergram
isBoxSelectedFlag
boolean isBoxSelectedFlag
- set by event handler mouse on click
selRow
int selRow
- selected row set by event handler mouse on click
selCol
int selCol
- selected column set by event handler mouse on click
iDataV
int iDataV
- col to norm by in [0:nDataV-1]
mouseModifiers
int mouseModifiers
- set by event handler mouse coords on click
xCursor
int xCursor
- x cursor set by event handler mouse coords on click
yCursor
int yCursor
- y cursor set by event handler mouse coords on click
selMID
int selMID
- set by event handler on click
selDist
float selDist
- distance selected by clicking on dendrogram
featuresStr
java.lang.String featuresStr
- current gene feature data
genomicDataStr
java.lang.String genomicDataStr
- current gene genomic data
boxX
int[] boxX
- ULHC event hlr [0:nCols-1]
boxY
int[] boxY
- ULHC event hlr [0:nRows-1]
colLabel
java.lang.String[] colLabel
- opt. column labels
rowLabel
java.lang.String[] rowLabel
- row labels (Master_ID + MasterGeneName)
rowMID
int[] rowMID
- row MID index
drawIntoImageFlag
boolean drawIntoImageFlag
- set if draw clustergram to GIF file
oGifFileName
java.lang.String oGifFileName
- GIF output file if used
mae
MAExplorer mae
- link to global instance
ms
MaHybridSample ms
- link to global MaHybridSample instance
fc
Filter fc
- link to global Filter instance
cdb
CompositeDatabase cdb
- link to global CompositeDatabase instance
epov
ExprProfileOverlay epov
- if ExprProfileOverlay is the parent, else null
spp
ShowPlotPopup spp
- if ShowPlotPopup is the parent, else null
olmap
OverlayMap olmap
- link to scatterplot named overlay maps instance
plotMode2D
int plotMode2D
- plot mode for spp
preferredHeight
int preferredHeight
- preferred canvas height
preferredWidth
int preferredWidth
- preferred canvas width
iWidth
int iWidth
- working canvas width
iHeight
int iHeight
- working canvas height
xDataScatterPlot
float[] xDataScatterPlot
- x Data for computing ratios when clicking
yDataScatterPlot
float[] yDataScatterPlot
- y Data for computing ratios when clicking
xPlotted
int[] xPlotted
- x plot coordinate for clicking on point in list
yPlotted
int[] yPlotted
- y plot coordinate for clicking on point in list
vx1
float vx1
- viewport x1 for clipping divider
vx2
float vx2
- viewport x2 for clipping divider
vy1
float vy1
- viewport y1 for clipping divider
vy2
float vy2
- viewport y2 for clipping divider
cx1
float cx1
- clipped x1 for clipping divider
cx2
float cx2
- clipped x2 for clipping divider
cy1
float cy1
- clipped y1 for clipping divider
cy2
float cy2
- clipped y2for clipping divider
cvPrecision
int cvPrecision
- fraction precision reporting data
nPointsPlotted
int nPointsPlotted
- # points plotted. # points= #genes X #samples
eventHandlerCL
GeneList eventHandlerCL
- set to gene list being used
gScatterPlot
java.awt.Graphics gScatterPlot
- Graphics context used with displayPlot
drawIntoImageFlag
boolean drawIntoImageFlag
- flag: set if draw plot to GIF file
oGifFileName
java.lang.String oGifFileName
- full Gif file path name
vertCaption
java.lang.String vertCaption
- ARGS: vertical caption
horizCaption
java.lang.String horizCaption
- ARGS: horizontal caption
title
java.lang.String title
- ARGS: horizontal caption
topTitle
java.lang.String topTitle
- ARGS:
title1
java.lang.String title1
- ARGS:
title2
java.lang.String title2
- ARGS:
title3
java.lang.String title3
- ARGS:
info1
java.lang.String info1
- ARGS:
info2
java.lang.String info2
- ARGS:
info3
java.lang.String info3
- ARGS:
info4
java.lang.String info4
- ARGS:
aText
java.lang.String aText
- ARGS:
aTextOrig
java.lang.String aTextOrig
- copy of original aText disp below title3
iFontSize
int iFontSize
- integer regular font size
iFontHdrSize
int iFontHdrSize
fontReg
java.awt.Font fontReg
- regular font
xText
int xText
- --
yText
int yText
- --
scaleX
double scaleX
- scale factor X-axis
scaleY
double scaleY
- scale factor X-axis
minX
double minX
- min X range set in initial call
maxX
double maxX
- max X range set in initial call
minY
double minY
- min Y range set in initial call
maxY
double maxY
- max X range set in initial call
minXscroll
double minXscroll
- min X range set by ShowPlotPopup scrollers
minYscroll
double minYscroll
- min Y range set by ShowPlotPopup scrollers
maxXscroll
double maxXscroll
- max X range set by ShowPlotPopup scrollers
maxYscroll
double maxYscroll
- max Y range set by ShowPlotPopup scrollers
showNonFilteredGenesFlag
boolean showNonFilteredGenesFlag
- show grayed out non-filtered genes
logScalingFlag
boolean logScalingFlag
- flag: Linear(false)/Log(true)
draw45lineFlag
boolean draw45lineFlag
- flag: draw 45 degree line
draw180lineFlag
boolean draw180lineFlag
- flag: draw 180 degree line
useXaxisIntNbrFlag
boolean useXaxisIntNbrFlag
- flag: label all vert lines w/int #
xScale
float xScale
- slope for xList to xPnt
yScale
float yScale
- slope for yList to yPnt
xBase
float xBase
- baseline for xxList to xPnt
yBase
float yBase
- baseline for yList to xyPnt
xList
float[] xList
- ALL of actual X data points to draw [0:nList-1]
yList
float[] yList
- ALL of actual Y data points to draw [0:nList-1]
xLineList
int[][] xLineList
- X values for only EGL gene points [0:nGroup-1][0:maxGenes-1]
yLineList
int[][] yLineList
- Y values for only EGL gene points [0:nGroup-1][0:maxGenes-1]
mapPntToMid
int[] mapPntToMid
- map point # in [0:nGroup*maxGenes] to [0:maxGenes]
jGrpList
boolean[] jGrpList
- group # for EP [0:maxGenes-1]
xPnt
int xPnt
- xList[] data mapped to int
yPnt
int yPnt
- yList[] data mapped to int
propList
int[] propList
- property of data to draw
dispCL
GeneList dispCL
- associated GeneList if not null
maxLineList
int maxLineList
- max allowed # of EGL genes
nList
int nList
- # elements in x(y)(p)List[0:nList-1]
nLineGroup
int nLineGroup
- # sequential points to connect group with line for use with EP 2D plot
# of lines/line-group
mae
MAExplorer mae
- link to global instance
spp
ShowPlotPopup spp
- Parent popup window instance
tree
HierClustNode tree
- cluster tree
title
java.lang.String title
- title for window
titlePanel
java.awt.Panel titlePanel
- titlePanel of parent
cgC
ClusterGramCanvas cgC
- Clustergram canvas
orderedCL
GeneList orderedCL
- GeneList being used
nGenes
int nGenes
- # genes in orderedCL
N_EP_GENES
int N_EP_GENES
- default # of genes to display in EP list
plotMode
int plotMode
- plot mode
nRows
int nRows
- # of rows in clustergram
nCols
int nCols
- # of columns in clustergram
curCGrow
int curCGrow
- current selected row of ClusterGram
curCGmid
int curCGmid
- current mid of selected ClusterGram row
nEPgenes
int nEPgenes
- # of genes to display in popup EP plot
statusCanvasHeight
int statusCanvasHeight
- height size of status canvas
drawDendroGramFlag
boolean drawDendroGramFlag
- set if draw dendrogram as well
keepFlagsOnClosing
boolean keepFlagsOnClosing
- mode of operation used in creating thiswindow for use in closing the window
statusCanvas
StatusCanvas statusCanvas
- status canvas
gGif
java.awt.Graphics gGif
- draw status at top of Gif image
dGramCheckBox
java.awt.Checkbox dGramCheckBox
- toggle drawing the dendrogram
saveAsGIF
java.awt.Button saveAsGIF
- Save display as GIF file
custGramReport
java.awt.Button custGramReport
- popup Report
zoomDgramButton
java.awt.Button zoomDgramButton
- zoom in on dendrogram
showHPnames
java.awt.Button showHPnames
- show list of Samples
showEPsubset
java.awt.Button showEPsubset
- show expression profiles for nEPgenes at current ClusterGram
position curCGrow
hierClustersExprProfPopup
ShowExprProfilesPopup hierClustersExprProfPopup
- exists if create EP plot subset popup
mae
MAExplorer mae
- link to global MAExplorer instance
ms
MaHybridSample ms
- link to global MaHybridSample instance
spp
ShowPlotPopup spp
- ARG: parent window
plotMode
int plotMode
- ARG: plot mode
mTitle
java.lang.String mTitle
- ARG: opt. title else generate one
preferredHeight
int preferredHeight
- preferred canvas height
preferredWidth
int preferredWidth
- preferred canvas width
binFreq
int[] binFreq
- [0:MAXBINS] bins frequency for display
binDataValue
float[] binDataValue
- [0:MAXBINS] bins actual value @start of bin for display
x1
int[] x1
- x1 [0:MAXBINS-1] for clicking on point in list
x2
int[] x2
- x2 [0:MAXBINS-1] for clicking on point in list
cvPrecision
int cvPrecision
- precision in intensity data report
iWidth
int iWidth
- working canvas width
iHeight
int iHeight
- working canvas height
oGifFileName
java.lang.String oGifFileName
- full Gif file path name
ncStr
java.lang.String ncStr
- Info on genes in the current bin
vertCaption
java.lang.String vertCaption
- vertical caption
horizCaption
java.lang.String horizCaption
- horizontal caption
horizVariableCaption
java.lang.String horizVariableCaption
- horizontal variable caption
title
java.lang.String title
- title
intensL
int intensL
- idx lower intensity range binDataValue[] space
intensU
int intensU
- idx upper intensity range binDataValue[] space
minFreq
int minFreq
- minimum range of values found in binFreq[]
maxFreq
int maxFreq
- maximum range of values found in binFreq[]
meanFreq
int meanFreq
- mean binFreq[]
medianFreq
int medianFreq
- median binFreq[]
meanBin
int meanBin
- mean bin intensity value for medianFreq
medianBin
int medianBin
- median bin intensity value for medianFreq
minBinX
int minBinX
- ARG: minimum possible value range set by scrollers
maxBinX
int maxBinX
- ARG: maximum possible value range set by scrollers
deltaBin
float deltaBin
- value of hist[] bin in [minX:maxX]
meanValue
float meanValue
- mean binFreq of weighted binFreq[]
medianValue
float medianValue
- median binFreq of binDataValue[]
modeH
float modeH
- set from ms hist[] statistics
medianH
float medianH
- set from ms hist[] statistics
minX
float minX
- ARG: minimum possible value range set by scrollers
maxX
float maxX
- ARG: maximum possible value range set by scrollers
pointType
int pointType
- point type: DRAW _PLUS, _CIRCLE, _BOX
hist
int[] hist
- freq hist[0:nHist-1].
activeBin
int activeBin
- active bin idx [0:MAXBINS-1] else -1
nHist
int nHist
- hist[0:nHist-1] of raw data. nHist should be MAExplorer.MAX_INTENSITY
drawIntoImageFlag
boolean drawIntoImageFlag
- set if draw plot to GIF file
outsideRangeFlag
boolean outsideRangeFlag
- for testing range
logScalingFlag
boolean logScalingFlag
- Linear(false)/Log(true)
smallFont
java.awt.Font smallFont
- font used for lableing
mae
MAExplorer mae
- link to global instance
cdb
CompositeDatabase cdb
- link to global instance
spp
ShowPlotPopup spp
- link to global instance
plotMode
int plotMode
- plot mode
pCanvas
java.awt.Canvas pCanvas
- canvas used to draw ratio histogram
preferredHeight
int preferredHeight
preferredWidth
int preferredWidth
x1
int[] x1
- X2 [1:nHist] for clicking on point in list
x2
int[] x2
- X2 [1:nHist] for clicking on point in list
binIndex
int[] binIndex
- corresponding hist bin index
iWidth
int iWidth
iHeight
int iHeight
oGifFileName
java.lang.String oGifFileName
- full Gif file path name
ncStr
java.lang.String ncStr
- Info on genes in the current bin
vertCaption
java.lang.String vertCaption
- vertical caption
horizCaption
java.lang.String horizCaption
- horizontal caption
horizVariableCaption
java.lang.String horizVariableCaption
- horizontal variable caption
title
java.lang.String title
- title
titleX
java.lang.String titleX
- X title
titleY
java.lang.String titleY
- Y title
minXfound
double minXfound
- min value of range of values found
maxXfound
double maxXfound
- min value of range of values found
minX
double minX
- ARG: minimum possible value range set by scrollers
maxX
double maxX
- ARG: maximum possible value range set by scrollers
pointType
int pointType
- point type: DRAW _PLUS, _CIRCLE, _BOX
histRatio
int[] histRatio
- freq bin hist[0:nHist-1].
histValue
double[] histValue
- value bin hist[0:nHist-1].
curXbinIdx
int curXbinIdx
- index of X axis for data arrays
activeBin
int activeBin
- active bin # [0:nHist] else -1
nHist
int nHist
- hist[0:npoints-1]
ratioLower
float ratioLower
- lower range of histogram values
ratioUpper
float ratioUpper
- upper range of histogram values
drawIntoImageFlag
boolean drawIntoImageFlag
- set if draw plot to GIF file
outsideRangeFlag
boolean outsideRangeFlag
- for testing range
logScalingFlag
boolean logScalingFlag
- Linear(false)/Log(true)
smallFont
java.awt.Font smallFont
- font used for lableing
mae
MAExplorer mae
- link to global instance
ms
MaHybridSample ms
- link to global instance
map
Maps map
- link to global instance
cdb
CompositeDatabase cdb
- link to global instance
plotMode
int plotMode
- plot mode of scatter plot
spp
ShowPlotPopup spp
- parent window
prevBestMID
int prevBestMID
- MID closest to point click on
mae
MAExplorer mae
- instance of MAExplorer so we can clear flags indicating
the user did a manual quit()
ep
ExprProfile ep
- expression profile for mid
preferredHeight
int preferredHeight
- preferred canvas height size
preferredWidth
int preferredWidth
- preferred canvas width size
xCursor
int xCursor
- event handler mouse X cursor coordinates
yCursor
int yCursor
- event handler mouse Y cursor coordinates
fontHeight
int fontHeight
- height font size of current font
fontLeading
int fontLeading
- leading font size of current font
title
java.lang.String title
- ARG: opt. from user. If drawLabel
plotStyleMode
int plotStyleMode
- plot mode style: 0=line, 1=circle, 2=curve
zoomBarsMag
int zoomBarsMag
- zoom magnification: by 1X, 2X, 5X, 10X, 20X mod
showKmeansDataFlag
boolean showKmeansDataFlag
- report K-means data else just CloneID & name
showErrBarsFlag
boolean showErrBarsFlag
- draw error bars for each line
doMeanPlotsFlag
boolean doMeanPlotsFlag
- mean else individual plots
didDataSetupFlag
boolean didDataSetupFlag
- set by setupData() if successful
drawLabelsFlag
boolean drawLabelsFlag
- ARG: draw labels for larger version
drawAdditionalDataFlag
boolean drawAdditionalDataFlag
- draw title & additional data if larger format.
drawIntoImageFlag
boolean drawIntoImageFlag
- set if draw plot to GIF file
oGifFileName
java.lang.String oGifFileName
- full Gif file path name
mae
MAExplorer mae
- links to global MAExplorer instance
sepp
ShowExprProfilesPopup sepp
- Parent window
title
java.lang.String title
- title for entire EP. panel
exprProfileCL
GeneList exprProfileCL
- GeneList being used
nGenes
int nGenes
- # genes in exprProfileCL
sbSize
int sbSize
- width of scroll bar control
prevBestMID
int prevBestMID
- save previous MID found with mouse
mNbr
int mNbr
- .mList[mNbr] in database to display
epOverlayList
ExprProfile[] epOverlayList
- list of overlay expr. profiles
d2dp
Draw2Dplot d2dp
- draw 2D overlay of EP plots
epplList
ExprProfilePanel[] epplList
- Expr Profs [nGridElements]
cTitle
java.lang.String[] cTitle
- titles [0:nGenes-1] "#Master_ID"
nHP_E
int nHP_E
- # of HPS in an Expr Profile
nMnGenes
int nMnGenes
- # of averaged genes ~ nGenes
hpDataNbrA
int[] hpDataNbrA
- # of samples for hpDataXXX[n][]
maxHPdataMn
float maxHPdataMn
- max of hpDataMnA[][] data
hpDataMnA
float[][] hpDataMnA
- mean[0:nMnGenes-1][0:nHP_E-1]
hpDataSDA
float[][] hpDataSDA
- S.D.[0:nMnGenes-1][0:nHP_E-1]
showErrBarsFlag
boolean showErrBarsFlag
- pass through to EP panel
doMeanPlotsFlag
boolean doMeanPlotsFlag
- if plot means and SD
hasMeanPlotsFlag
boolean hasMeanPlotsFlag
- if hpDataXXX[] exists
plotStyleMode
int plotStyleMode
- plot style mode: 0=line, 1=circle, 2=curve
zoomBarsMag
int zoomBarsMag
- zoom factor: 1X, 2X, 5X, 10X pass through to EP panel
epPanel
java.awt.Panel epPanel
- holds g2D overlay plot
hsL
java.awt.Scrollbar hsL
- lower bound horizontal scroll bar
hsU
java.awt.Scrollbar hsU
- upper bound horizontal scroll bar
vsL
java.awt.Scrollbar vsL
- lower bound vertical scroll bar
vsU
java.awt.Scrollbar vsU
- upper bound vertical scroll bar
maxHsteps
int maxHsteps
- # of steps for hsL hsU
maxVsteps
int maxVsteps
- # of steps for vsL vsU
hLB
float hLB
- lower HP sample # to display
hUB
float hUB
- upper HP sample # to display
vLB
float vLB
- lower expression value to display
vUB
float vUB
- upper expression value to display
xList
float[] xList
- [nGenes*nHP_E] EP overlay X coords
yList
float[] yList
- [nGenes*nHP_E] EP overlay Y coords
nPoints
int nPoints
- nGenes*nHP_E
propList
int[] propList
- [nGenes*nHP_E] EP overlay props
mapPointToMid
int[] mapPointToMid
- [nGenes*nHP_E] mid mapping
epOvrLayCL
GeneList epOvrLayCL
- special [nGenes*nHP_E] CL
bestGene
Gene bestGene
- gene if mouse event
bestHP
int bestHP
- HP if mouse event
bestMid
int bestMid
- gene clone ID if mouse event
bestIntens
float bestIntens
- intensity if mouse event
mae
MAExplorer mae
- link to global MAExplorer instance
epc
ExprProfileCanvas epc
- expression profile canvas we put into panel
mae
MAExplorer mae
- link to global MAExplorer instance
eppl
ExprProfilePanel eppl
- panel we put into this popup window
preferredHeight
int preferredHeight
- prefered height canvas size, 0 to use defaults
preferredWidth
int preferredWidth
- prefered width canvas size, 0 to use defaults
showErrBarsCheckBox
java.awt.Checkbox showErrBarsCheckBox
- checkbox to show error bars
saveAsGIF
java.awt.Button saveAsGIF
- Save display as GIF file
plotStyleButton
java.awt.Button plotStyleButton
- plot style (line, circle, curve) button
zoomBarsButton
java.awt.Button zoomBarsButton
- zoom magnification button
addButtonsFlag
boolean addButtonsFlag
- flag: if false, don't add title or Close button
mae
MAExplorer mae
- link to global MAExplorer instance
sepp
ShowExprProfilesPopup sepp
- Parent window
title
java.lang.String title
- title for entire EP. panel
exprProfileCL
GeneList exprProfileCL
- GeneList being used
nGenes
int nGenes
- # genes in exprProfileCL
N_EP_GENES
int N_EP_GENES
sbSize
int sbSize
- width of scroll bar control
nGridElements
int nGridElements
- i.e. nRows*nCols
nRows
int nRows
- # of rows in the Grid
nCols
int nCols
- # of columns in the Grid
mNbr
int mNbr
- .mList[mNbr] in database to display
nEPgenes
int nEPgenes
- # genes to display in popup EP plot
epOverlayList
ExprProfile[] epOverlayList
- list of overlay expr. profiles
epplList
ExprProfilePanel[] epplList
- Expr Profs [nGridElements]
cTitle
java.lang.String[] cTitle
- [0:nGenes-1] "#Master_ID"
nHP_E
int nHP_E
- # of HPS in an Expr Profile
nMnGenes
int nMnGenes
- # of averaged genes ~ nGenes
hpDataNbrA
int[] hpDataNbrA
- # of samples for hpDataXXX[n][]
maxHPdataMn
float maxHPdataMn
- max of hpDataMnA[][] data
hpDataMnA
float[][] hpDataMnA
- mean[0:nMnGenes-1][0:nHP_E-1]
hpDataSDA
float[][] hpDataSDA
- S.D.[0:nMnGenes-1][0:nHP_E-1]
showErrBarsFlag
boolean showErrBarsFlag
- pass through to EP panel
doMeanPlotsFlag
boolean doMeanPlotsFlag
- if plot means and SD
hasMeanPlotsFlag
boolean hasMeanPlotsFlag
- if hpDataXXX[] exists
plotStyleMode
int plotStyleMode
- plot style mode: 0=line, 1=circle, 2=curve
zoomBarsMag
int zoomBarsMag
- 1X, 2X, 5X, 10X pass through to EP panel
epPanel
java.awt.Panel epPanel
- holds grid of ExprProfilePanel's
vs
java.awt.Scrollbar vs
- vertical scroll bar
xList
float[] xList
- [nGenes*nHP_E] EP overlay coords
yList
float[] yList
- [nGenes*nHP_E] EP overlay coords
nPoints
int nPoints
- nGenes*nHP_E
propList
int[] propList
- [nGenes*nHP_E] EP overlay props
epOvrLayCL
GeneList epOvrLayCL
- special [nGenes*nHP_E] CL
bestGene
Gene bestGene
- gene if mouse event
bestHP
int bestHP
- HP if mouse event
bestMid
int bestMid
- gene clone ID if mouse event
bestIntens
float bestIntens
- intensity if mouse event
|
Class Guesser implements Serializable |
mae
MAExplorer mae
- link to global instance
map
Maps map
- link to global Maps instance
mbf
MenuBarFrame mbf
- link to global MenuBarFrame instance
gipo
GipoTable gipo
- link to global GipoTable instance
frame
java.awt.Frame frame
- frame where guesser is built
ta
java.awt.TextArea ta
- TextArea list of best guesses
tf
java.awt.TextField tf
- Text field for User input
buttonPanel
java.awt.Panel buttonPanel
- place for buttons
titlePanel
java.awt.Panel titlePanel
- place for title
titleLabel
java.awt.Label titleLabel
- title label
geneDBnamesButton
java.awt.Button geneDBnamesButton
- toggle: "Master ID", "GeneName", "GenBank", "dbEst", "UniGene", "LocusID"
kev
KeyEventHandler kev
- handle events for text field
meh
MouseEventHandler meh
- handle events for text area
resultStr
java.lang.String resultStr
- return user results from guesser
title
java.lang.String title
- title of window
alphaListMode
java.lang.String alphaListMode
- "GeneName", "GenBank", "dbEst" etc
resultSubList
java.lang.String[] resultSubList
- if passing results back as sublist
alphaList
java.lang.String[] alphaList
- char text to be searched (GeneName)
sortedAlphaListStr
java.lang.String sortedAlphaListStr
- concatenated string for sorting
alphaListSize
int alphaListSize
- size of alphaList array
subAlphaList
java.lang.String[] subAlphaList
- sub strings for guesser
onceOnlyFlag
boolean onceOnlyFlag
- global setup flag
genericFlag
boolean genericFlag
- if true, don't put Clone opt. button
setEGLfromListFlag
boolean setEGLfromListFlag
- if set then group copy to EGL
geneIDname
java.lang.String[] geneIDname
- button labels
iMode
int iMode
- one of the above MODE_xxxx values
resultMode
int resultMode
- what type of finish was requested: either SINGLE_GENE or MULTIPLE_GENE
maxGenes
int maxGenes
- local map.maxGenes
taRows
int taRows
- size of TextArea
taCols
int taCols
- size of TextArea
chFirstTyped
char chFirstTyped
- first char typed
font
java.awt.Font font
- Font for guesser list
pgcg
PopupGeneGuesser pgcg
- parent class instance if it is not null
phpmg
PopupHPmenuGuesser phpmg
- parent class instance if it is not null
pPDg
PopupProjDirGuesser pPDg
- parent class instance if it is not null
frameBkGrdColor
java.awt.Color frameBkGrdColor
- Background color of entire frame
textBkGrdColor
java.awt.Color textBkGrdColor
- background color of text area
buttonBkGrdColor
java.awt.Color buttonBkGrdColor
- background color of buttons
area
java.awt.TextArea area
- Text area for displaying the text
hideButton
java.awt.Button hideButton
- hide button to hide the Log window. You need to issue a command
from the MAExplorer menu to get it back).
saveAsButton
java.awt.Button saveAsButton
- Save Log As button to save the log data as a new named Report/XXXX.txt file
clearButton
java.awt.Button clearButton
- clear button to clear the log and clear the log file is using a file
layout
java.awt.GridBagLayout layout
- GUI layout
constraints
java.awt.GridBagConstraints constraints
- grid bag constraints
default_font
java.awt.Font default_font
- default font
button_font
java.awt.Font button_font
- control button font
text_font
java.awt.Font text_font
- text font in TextArea
title
java.lang.String title
- text to beas popup window title
logTextStr
java.lang.String logTextStr
- text to be written to text area
appendLogDataFlag
boolean appendLogDataFlag
- Flag indicating that data is to be appended text area.
If it is not being appended to text area, it is at least appended
to the logTextStr.
isVisibleFlag
boolean isVisibleFlag
- Visibility flag
logFile
java.io.File logFile
- optional log file if logging
logFileName
java.lang.String logFileName
- optional log file "maeHistory.log"
fullLogFilePath
java.lang.String fullLogFilePath
- optional full path of log file if it exists.
logFileWriter
java.io.FileWriter logFileWriter
- standalone log file writer
logDataBuf
char[] logDataBuf
- standalone log file data buff
logDataBufSize
int logDataBufSize
- size of standalone log file data buff
onceOnlyFlag
boolean onceOnlyFlag
- flag to prevent multiple instances
gnp
GenNormalizationPlugin gnp
- Only while debugging: if DBUG_GENERIC_NORM_PLUGIN is set for use with
TestPlugin.
LECBdebug
int LECBdebug
- Developer debug flag. This is 0 if debugging, -1 otherwise and is
used for building menus while developing code. We set it to 0 either
explicitly or by the DEBUG flag.
applet
java.applet.Applet applet
- "this" applet instance for MAExplorer main class
previousStartupState
boolean previousStartupState
- Flag that indicates if the startup .mae file exists in PREVIOUS database
configFile
java.lang.String configFile
- Default Configuration file: "MaExplorerConfig.txt"
is
ArrayScroller is
- Global instance of ArrayScroller obj to hold pseudoarray image
scrollable canvas
clg
ClusterGenes clg
- Global instance of Cluster Genes object
cdb
CompositeDatabase cdb
- Global instance of composite database object
cdList
Condition cdList
- Global instance of condition list tables
cfg
Config cfg
- Global instance of Configuration and state variables including top level
file, URL configs, etc.
cfgDB
ConfigTable cfgDB
- Global instance of configuration data from MaExplorerConfig.txt file
grcd
GridCoords grcd
- Global instance of share grid coordinate mapper
dwPI
DrawPseudoImage dwPI
- Global instance of draw pseudo image
egl
EditedGeneList egl
- Global instance of edit editedCL gene (clone) list
em
EventMenu em
- Global instance of handle MenuItem and MenuItemCheckbox events
fio
FileIO fio
- Global instance of file and URL I/O
fc
Filter fc
- Global instance of data Filter gene operations
gene
Gene gene
- Global instance of Gene
gct
GeneClass gct
- Global instance of Gene Class table
ccd
GeneGeneDist ccd
- Global instance of Gene-Gene distances
clLst
GeneList clLst
- Global instance of GeneList contains gene (clone) list tables
gipo
GipoTable gipo
- Global instance of GIPO table mapping genes to other data
gp
GetParams gp
- Global instance of contains set of applet/configuration PARAM parsers
infoDB
MaInfoTable infoDB
- Global instance of depricated "MaExplorerInfo.txt" DB list of .info data
for entire DB.
mp
Maps mp
- Global instance of lookup table maps populated elsewhere
mbf
MenuBarFrame mbf
- Global instance of Frame based MenuBar
olmap
OverlayMap olmap
- Global instance of scatterplot named overlay maps
pur
PopupRegistry pur
- Global instance of holds popup registry of all active popup windows and
update handlers.
hps
SampleSets hps
- Global instance of HP-X, HP-Y and HP-E sets and lists
sampDB
SamplesTable sampDB
- The "Samples.txt" database list of the H.P.s in the entire database.
sd
SpotData sd
- Global instance of spot data object
sf
SpotFeatures sf
- Global instance of spot feature info
sg
StageNames sg
- Global instance of Staging names for menus etc
stateScr
StateScrollers stateScr
- holds popup state scrollers - note: created in MenuBarFrame!
stat
Statistics stat
- Global instance of parametric & non-parametric stats
us
UserState us
- Global instance of User State methods
util
Util util
- Global instance of Utility class
clstrSamp
ClusterSamples clstrSamp
- Global instance of ClusterSamples class
dryRotExcept
DryRotException dryRotExcept
- Global instance of DryRotException class
classNameX
java.lang.String classNameX
- "HP-X 'set'" name for msListX[] HPs
classNameY
java.lang.String classNameY
- "HP-Y 'set'" name for msListY[] HPs
scrWidth
int scrWidth
- Horizontal screen size
scrHeight
int scrHeight
- Horizontal screen size
proxyServer
java.lang.String proxyServer
- base addr PARAM "proxyServer"
maeServerBase
java.lang.String maeServerBase
- top level codebase for MAE server
docCodeBase
java.lang.String docCodeBase
- codebase where the documentation Reference Manual is kept
fileSeparator
java.lang.String fileSeparator
- paths, "/" or "|", depends on OS
dynFileSeparator
java.lang.String dynFileSeparator
- dynamic paths separator, "/" or "|", depends on OS and if using
URL from Stand-Alone
defSAprjName
java.lang.String defSAprjName
- Standalone current project DB name
cacheDir
java.lang.String cacheDir
- Standalone /Cache directory for saving data downloaded for array
Web server.
reuseGUIframeFlag
boolean reuseGUIframeFlag
- Flag: set if reuse main GUI frame
isWinPCflag
boolean isWinPCflag
- Flag: set to TRUE if any Windows PC
otherUserName
java.lang.String otherUserName
- access other user name from Dialog
userName
java.lang.String userName
- Dialog: current user login name
userPasswd
java.lang.String userPasswd
- Dialog: current user password
validPrj
java.lang.String[] validPrj
- [0:n-1] login verified projects
nValidPrj
int nValidPrj
- # of login verified projects
isLoggedInFlag
boolean isLoggedInFlag
- set if valid login has been performed
userStateName
java.lang.String userStateName
- current user state name
userStateIdx
int userStateIdx
- current user state index
pImage
java.awt.Image pImage
- pseudo grayscale microarray image based on .quantspot intensity data.
This image is shared by ALL HPs and is recompute if current HP
changes.
pWidth
int pWidth
- working size of pseudoarray image
pHeight
int pHeight
- working size of pseudoarray image
MAX_INTENSITY
int MAX_INTENSITY
- maximum # intensity values of .quant data
maxPreloadImgs
int maxPreloadImgs
- PARAM max # images to preload set from "maxPreloadImages"
iSampleName
java.lang.String[] iSampleName
- HP name from "image*" [1:iHPnbr] allocated [MAX_HYB_SAMPLES+1]
iImageFile
java.lang.String[] iImageFile
- image files to read allocated [MAX_HYB_SAMPLES+1]
iHPnbr
int iHPnbr
- # of entries in "image#" PARAM list. The mae.hps.msList[1:mae.hps.nHP]
is derived from this and modified from snHPName[] list.
snHPnbr
int snHPnbr
- # of entries in the Stage name list
mapHPtoMenuName
int[] mapHPtoMenuName
- index of snHPName[] corresponding to iSampleName[] entry
allocated [MAX_HYB_SAMPLES+1].
snHPName
java.lang.String[] snHPName
- slist of tage HP name [1:snHPnbr]
snHPSampleID
java.lang.String[] snHPSampleID
- list of free form sample names [1:snHPnbr]
snHPDatabaseFileID
java.lang.String[] snHPDatabaseFileID
- (opt) list of DB file ID [1:snHPnbr]
snImageFile
java.lang.String[] snImageFile
- list of image files to read [1:snHPnbr]
snHPMenuText
java.lang.String[] snHPMenuText
- list for building menus [1:snHPnbr]
snHPFullStageText
java.lang.String[] snHPFullStageText
- list for buildingn menus [1:snHPnbr]
snPrjName
java.lang.String[] snPrjName
- list of Project names [1:snHPnbr]
snNeedLogin
boolean[] snNeedLogin
- (opt) sample requires login
snSwapCy5Cy3Data
boolean[] snSwapCy5Cy3Data
- swap (Cy3,Cy5) field data for (Cy5,Cy3) for this HP
sortedGeneAndCloneIDListsFlag
boolean sortedGeneAndCloneIDListsFlag
- true if alphaList[] geneNames and numericList[] gene xxxx_IDs are sorted
nFilesRead
int nFilesRead
- # of files read so far
nFilesTotal
int nFilesTotal
- # files always read + # .quant files. i.e. = N_CONST_FILES +
N_EST_QUANT_FILES.
runLoopDelayMsec
int runLoopDelayMsec
- Flicker delay for run() loop delay also used for flicker
runT
java.lang.Thread runT
- main thread for run()
spotRad
int spotRad
- PARAM "SpotRadius"
sit1
float sit1
- PARAM "SI1" 0 or MIN_INTENSITY (spot Intens.)
sit2
float sit2
- PARAM "SI2" MAX_INTENSITY
t1
float t1
- PARAM "I1" 0 or MIN_INTENSITY (gene "intens")
t2
float t2
- PARAM "I2" MAX_INTENSITY
r1
float r1
- PARAM "R1" MIN_RATIO range (HP-X/HP-Y)
r2
float r2
- PARAM "R2" MAX_RATIO range
cr1
float cr1
- PARAM "CR1" MIN_RATIO range (i.e. Cy3/Cy5)
cr2
float cr2
- PARAM "CR2" MAX_RATIO range
rptFontSize
java.lang.String rptFontSize
- Report font size: "8pt", "10pt", or "12pt"
dryrotLogStr
java.lang.String dryrotLogStr
- List of dryrot messages if any occur. Should be null.
showEGLflag
boolean showEGLflag
- Display Flag: show edited gene list
mReady
boolean mReady
- Flag set when done initialization and ready to analyze
isWorkingMAE
boolean isWorkingMAE
- Flag indicating whether using the Working server (mae/) or not
plotImageMode
int plotImageMode
- Pseudo array image plot mode: PLOT_xxxx_IMAGE
editMode
int editMode
- EGL mode for 'edited gene list': EDIT_xxxx
hierClustMode
int hierClustMode
- Hier.Clustering linkage mode: HIER_CLUST_xxxxx
qualTypeMode
int qualTypeMode
- spot quality type mode: QUALTYPE_xxxx
posQuantTestMode
int posQuantTestMode
- positive Quant data test mode: SS_MODE_xxxx
goodSpotTestMode
int goodSpotTestMode
- Good Spot (QualChk) test mode: SS_MODE_xxxx
detValueSpotTestMode
int detValueSpotTestMode
- Spot (Detection Value) test mode: SS_MODE_xxxx
reportMode
int reportMode
- Report type mode: RPT_xxxx. Not saved in state
tblFmtMode
int tblFmtMode
- Report table format mode: RPT_FMT_xxxx
spotIntensTestMode
int spotIntensTestMode
- spot intensity test mode: SS_MODE_xxxx
spotIntensRangeMode
int spotIntensRangeMode
- Spot intensity range mode for thresholds RANGE_OUTSIDE, RANGE_INSIDE
spotIntensCompareMode
int spotIntensCompareMode
- Spot Intensity compare mode for threshold: COMPARE_xxxx
sampleIntensityRangeMode
int sampleIntensityRangeMode
- Sample intensity range mode for threshold: RANGE_INSIDE, RANGE_OUTSIDE
ratioRangeMode
int ratioRangeMode
- Ratio range restriction for threshold mode: RANGE_INSIDE, RANGE_OUTSIDE
ratioCy3Cy5RangeMode
int ratioCy3Cy5RangeMode
- Cy3/Cy5 range restriction for threshold mode: RANGE_INSIDE, RANGE_OUTSIDE
cvTestMode
int cvTestMode
- CV test mode: SS_MODE_xxxx
isAppletFlag
boolean isAppletFlag
- Flag: cleared if enter through standalone main()
useWebDBflag
boolean useWebDBflag
- Flag: stand-alone PARAM "useWebDB" try WebDB before local directories
enableFIOcachingFlag
boolean enableFIOcachingFlag
- Flag: stand-alone PARAM "enableFIOcaching"
cacheFIOflag
boolean cacheFIOflag
- Flag: if enabled, it first checks the /Cache directory for all http://
codebase files and if not in the cache, it saves the file in the
cache after reading it from the Web.
madeChangesFlag
boolean madeChangesFlag
- made changes to DB so may want to SAVE DB
useCy5OverCy3Flag
boolean useCy5OverCy3Flag
- PARAM "useCy5/Cy3" else Cy3/Cy5
useMouseOverFlag
boolean useMouseOverFlag
- PARAM "useMouseOver" for popup tracking balloons
flickerXYflag
boolean flickerXYflag
- Flicker HP-X and HP-Y in run() loop
lowRangeZoomFlag
boolean lowRangeZoomFlag
- Scale pseudoarray image by 1/100 to zoom low-range values
isZscoreFlag
boolean isZscoreFlag
- Flag: is using one of the Zscore normalizations
useEPoverlayFlag
boolean useEPoverlayFlag
- Flag: Plot EP list as overlay 2Dplot else scrollable Grid of EPs
swapRowsColsFlag
boolean swapRowsColsFlag
- PARAM flip array rows & columns
useRatioDataFlag
boolean useRatioDataFlag
- PARAM "useRatioData" Cy3/Cy5 else Intensity
useHPxySetDataFlag
boolean useHPxySetDataFlag
- use HP-X,Y 'sets msListX/Y else HP-X,HP-Y msX/Y
useMeanHPeListDataFlag
boolean useMeanHPeListDataFlag
- [TODO] use mean HP-E 'list' data else single current HP sample data
allowNegQuantDataFlag
boolean allowNegQuantDataFlag
- PARAM "allowNegQuantDataFlag"
updatePseudoImgFlag
boolean updatePseudoImgFlag
- update pseudo image - not saved in the State
usePseudoXYcoordsFlag
boolean usePseudoXYcoordsFlag
- PARAM use Pseudo XY coords else actual
dualXYpseudoPlotFlag
boolean dualXYpseudoPlotFlag
- Flag: plot mean HP-X in F1, HP-Y in F2 pseudoimg
reuseXYcoordsFlag
boolean reuseXYcoordsFlag
- Flag: reuse HP[1] Quant xy coords for speedup
noMsgReportFlag
boolean noMsgReportFlag
- PARAM "noMsgReporting"
dieFlag
boolean dieFlag
- Flag: call quit() if flag set to exit run(). Not saved in state
abortFlag
boolean abortFlag
- Flag: set true by the STOP button. Not saved in state
doGCflag
boolean doGCflag
- Flag: run the Garbage Collector. Not saved in state
killAppletFlag
boolean killAppletFlag
- Flag: set if do "Quit". Not saved in state
viewFilteredSpotsFlag
boolean viewFilteredSpotsFlag
- Flag: show Filtered spots
useDichromasyFlag
boolean useDichromasyFlag
- PARAM "useDichromasy" alt. colors
gangSpotFlag
boolean gangSpotFlag
- Flag: report f1 or f1&f2 (ganged)
presentViewFlag
boolean presentViewFlag
- Flag: use larger fonts, thicker lines, circles, plus, etc. for
presentation viewing
useSPLUSasComputingEngineFlag
boolean useSPLUSasComputingEngineFlag
- Flag: Use S-PLUS, else R, as computing engine
useRLOloggingFlag
boolean useRLOloggingFlag
- Flag: use time-stamped RLO logging files folders, else just Report/
masterGeneName
java.lang.String masterGeneName
- either "GeneName", "UGclusterName, etc"
masterIDname
java.lang.String masterIDname
- either "CloneID", "UniGeneID, GenBank, etc"
masterNameMode
int masterNameMode
- either MASTER_GENE_NAME or MASTER_UG_NAME
masterIDmode
int masterIDmode
- either MASTER_CLONE_ID or MASTER_GENBANK or MASTER_GENBANK5 or
MASTER_GENBANK3 or MASTER_UG_ID, MASTER_SWISS_PROT, MASTER_GENERIC_ID
reportRatioStr
java.lang.String reportRatioStr
- either "F1/F2", "Cy3/Cy5", or "Cy5/Cy3"
normNameDisp
java.lang.String normNameDisp
- name of norm. method in Status display
normName
java.lang.String normName
- name of normalization method
useGoodSpotsForGlobalStatsFlag
boolean useGoodSpotsForGlobalStatsFlag
- use Good Spots data for computing global array statistics for
normalization purposes on a per array basis,
otherwise use all spot data.
bkgdCorrectFlag
boolean bkgdCorrectFlag
- calc: I'= Intensity - background
ratioMedianCorrectionFlag
boolean ratioMedianCorrectionFlag
- enable cy3/cy5 ratio median correction
normByHousekeepGenesFlag
boolean normByHousekeepGenesFlag
- normalize by housekeeping genes
normByGeneSetFlag
boolean normByGeneSetFlag
- normalize by 'user gene set'
normByCalDNAflag
boolean normByCalDNAflag
- normalize by Calibration DNA set
normByZscoreFlag
boolean normByZscoreFlag
- normalize by HP Zscore
normByMedianFlag
boolean normByMedianFlag
- normalize by HP median
normByLogMedianFlag
boolean normByLogMedianFlag
- normalize by HP log of median
normByZscoreMeanStdDevLogFlag
boolean normByZscoreMeanStdDevLogFlag
- norm by Zscore log intens,stdDev.
normByZscoreMeanAbsDevLogFlag
boolean normByZscoreMeanAbsDevLogFlag
- norm. by Zscore log intens,meanAbsDev
scaleDataToMaxIntensFlag
boolean scaleDataToMaxIntensFlag
- normalize to maximum intensity
testGenericNormPluginFlag
boolean testGenericNormPluginFlag
- If DBUG_GENERIC_NORM_PLUGIN, then debug GenericNormalizationPlugin
within the code. If the DBUG_GENERIC_NORM_PLUGIN is enabled, then
the GenNormalizationPlugin) gnp will exist and point to the instance.
The menu item appears in the menu:
(Analysis | Normalization | "Test Generic Norm Plugin [DBUG]")
useCorrCoeffFlag
boolean useCorrCoeffFlag
- use correlation coeffieient instead of Euclidian distance when clustering
hierClustUnWtAvgFlag
boolean hierClustUnWtAvgFlag
- use UPGMA or WPGMA for computing the average node vector when hierarchical
clustering.
normHCbyRatioHPflag
boolean normHCbyRatioHPflag
- set true if normalize Hier-Clustering dataV[h] by dataV[iDataV]
else norm by HP[h] msListE[h].maQ.maxRI
useMedianForKmeansClusteringFlag
boolean useMedianForKmeansClusteringFlag
- set true if use median instead of means of clusters in K-means clustering.
genBankViewerFlag
boolean genBankViewerFlag
- GenBank popup browser Mode
dbESTviewerFlag
boolean dbESTviewerFlag
- dbEST popup browser Mode
uniGeneViewerFlag
boolean uniGeneViewerFlag
- UniGene popup browser Mode
omimViewerFlag
boolean omimViewerFlag
- OMIM popup browser Mode
mAdbViewerFlag
boolean mAdbViewerFlag
- mAdb Clone page popup browser Mode
locusLinkViewerFlag
boolean locusLinkViewerFlag
- LocusLink LocusID page popup browser Mode
medMinerViewerFlag
boolean medMinerViewerFlag
- MedMiner gene page popup browser Mode
swissProtViewerFlag
boolean swissProtViewerFlag
- Swiss-Prot page popup browser Mode
pirViewerFlag
boolean pirViewerFlag
- PIR page popup browser Mode
genomicViewerFlag
boolean[] genomicViewerFlag
- holds sGenomicMenu[cfg.nGenomicMenus] menu flags
useEPrawIntensValFlag
boolean useEPrawIntensValFlag
- use Raw intensity for EP ratios in gene REPORTS
addExprProfileFlag
boolean addExprProfileFlag
- set for EP ratios in gene REPORTS
addHP_XYstatFlag
boolean addHP_XYstatFlag
- set for HP_XY statistics in gene REPORTS
addOCLstatFlag
boolean addOCLstatFlag
- set for OCL statics statistics in gene REPORTS
autoStateScrPopupFlag
boolean autoStateScrPopupFlag
- Auto state-scroller popup windown assoc w/Filters
useLowRatiosFilterFlag
boolean useLowRatiosFilterFlag
- "Use lowest X/Y ratios filter"
useHighRatiosFilterFlag
boolean useHighRatiosFilterFlag
- "Use highest X/Y ratios filter"
spotIntensFilterFlag
boolean spotIntensFilterFlag
- filter genes by spot Intensity threshold
intensFilterFlag
boolean intensFilterFlag
- filter genes by intensity threshold
ratioFilterFlag
boolean ratioFilterFlag
- filter genes by ratio threshold
ratioCy3Cy5FilterFlag
boolean ratioCy3Cy5FilterFlag
- filter genes by Cy3/Cy5 ratio threshold
geneClassMbrFilterFlag
boolean geneClassMbrFilterFlag
- filter genes by GeneClass mbrshp
useGeneSetFilterFlag
boolean useGeneSetFilterFlag
- filter genes by useGeneSet mbrship
useRatioHistCLflag
boolean useRatioHistCLflag
- filter genes on Ratio histogram bin
useIntensHistCLflag
boolean useIntensHistCLflag
- filter genes on Intensity hist bin
useEditedCLflag
boolean useEditedCLflag
- filter genes on Edited Gene List
useGoodGeneCLflag
boolean useGoodGeneCLflag
- filter by genes in Good Genes List
useReplicateGenesFlag
boolean useReplicateGenesFlag
- filter by genes with at least 1 replicate
useCVmeanElseMaxFlag
boolean useCVmeanElseMaxFlag
- use mean of CV else use max in CV filter
tTestXYfilterFlag
boolean tTestXYfilterFlag
- filter genes passing HP-X/-Y t-test
tTestXYsetsFilterFlag
boolean tTestXYsetsFilterFlag
- filter genes passing HP-X/-Y sets t-test
KS_TestXYsetsFilterFlag
boolean KS_TestXYsetsFilterFlag
- filter genes passing HP-X/-Y sets KS-test
F_TestOCLFilterFlag
boolean F_TestOCLFilterFlag
- filter genes passing current OCL (Ordered Condition List) F-test
useSpotCVfilterFlag
boolean useSpotCVfilterFlag
- filter by Spot CV filter is enabled
clusterHP_EfilterFlag
boolean clusterHP_EfilterFlag
- filter genes by cluster HP-E
useDiffFilterFlag
boolean useDiffFilterFlag
- filter genes by abs diff(HP-X,HP-Y)
usePosQuantDataFlag
boolean usePosQuantDataFlag
- filter genes with positive quant data
useGoodSpotDataFlag
boolean useGoodSpotDataFlag
- filter genes with Good Spot (QualChk) data
useDetValueSpotDataFlag
boolean useDetValueSpotDataFlag
- filter genes with Spot (Detection value) data
useOnlyGenesWithNonZeroDensityFlag
boolean useOnlyGenesWithNonZeroDensityFlag
- filter by genes with non-zero intensity - problem when do log() transform
clusterOnFilteredCLflag
boolean clusterOnFilteredCLflag
- cluster on Filtered/All genes
useClusterDistFlag
boolean useClusterDistFlag
- cluster distance thresholding
useSimGeneClusterDispFlag
boolean useSimGeneClusterDispFlag
- show a cluster of similar genes for current gene
useClusterCountsDispFlag
boolean useClusterCountsDispFlag
- show gene clusters count
useHierClusterDispFlag
boolean useHierClusterDispFlag
- show hierarchical clusters
useKmeansClusterCntsDispFlag
boolean useKmeansClusterCntsDispFlag
- show K-means clusters
useLSQmagNormFlag
boolean useLSQmagNormFlag
- norm geneEPvect[] to 1.0 for clustering
useClusterDistCacheFlag
boolean useClusterDistCacheFlag
- use cluster cache else recompute each time
useShortClusterDistCacheFlag
boolean useShortClusterDistCacheFlag
- use short else float cluster cache, can save memory if really needed
mae
MAExplorer mae
- link to global instance
cfg
Config cfg
- link to global Config instance
title
java.lang.String title
- title for frame
nMenuStubs
int nMenuStubs
- # of menu stubs in the list
stubNames
java.lang.String[] stubNames
- list of Names of Stubs in Menu tree
stubMenus
java.awt.Menu[] stubMenus
- list of Menu Stubs in Menu tree
rloSmnu
java.awt.Menu rloSmnu
- Menu stub to add/modify R(Plugin | RLO methods (submenu)) menu items
nRLOs
int nRLOs
- # of RLO entries in the menu
rloMenuNames
java.lang.String[] rloMenuNames
- RLO menu names [0:nRLOs-1] in Plugin | RLO methods) menu tree
rloRscriptNames
java.lang.String[] rloRscriptNames
- RLO menu names [0:nRLOs-1] in Plugin | RLO methods) menu tree
aTitle
java.lang.String aTitle
- i.e. mae.browserTitle
x0
int x0
- ULHC X of MenuBarFrame window
y0
int y0
- ULHC X of MenuBarFrame window
reportLabel
java.awt.Label reportLabel
- report label must be global variable
smallFontLbl
java.awt.Font smallFontLbl
- current global small font
mediumFontLbl
java.awt.Font mediumFontLbl
- current global medium font
useFontLbl
java.awt.Font useFontLbl
- current global font to use font
exprProfilePopup
ExprProfilePopup exprProfilePopup
- command pops it up
dialogFrame
java.awt.Frame dialogFrame
- dialog frame created but not displayed until needed
pdq
PopupDialogQuery pdq
- holds popup dialog query
pBOdq
PopupBinOprDialogQuery pBOdq
- holds popup BinOpr dialog query
HPlabelPanel
java.awt.Panel HPlabelPanel
- holds HP-X & -Y labels, STOP button
ps
java.awt.Panel ps
- holds above chkboxes & scrollbar panels
stopButton
java.awt.Button stopButton
- If hasStopButtonFlag is set (i.e. button exists, then set if want to abort
a computation. The event handler sets the mae.abortFlag
mouseOverCheckBox
java.awt.Checkbox mouseOverCheckBox
- Show Mouse-over info
curGeneTextButton
java.awt.Button curGeneTextButton
- enter cur. gene name in popup guesser
masterIDguesserIsPoppedUp
boolean masterIDguesserIsPoppedUp
- if guesser was popped up
gnMidGuesser
PopupGeneGuesser gnMidGuesser
- create when needed
hasStopButtonFlag
boolean hasStopButtonFlag
- set if stopButton has "STOP!" label
hpMenuChooserIsPoppedUp
boolean hpMenuChooserIsPoppedUp
- if chooser was popped up
hpMenuGuesserIsPoppedUp
boolean hpMenuGuesserIsPoppedUp
- if guesser was popped up
stopLblName
java.lang.String stopLblName
- either "STOP!" or " "
hpMenuToUpdateFromGuesser
java.lang.String hpMenuToUpdateFromGuesser
- Set in event handler to one of: ":HP" ":HP_X" ":HP_Y" ":HP_X+" ":HP_X-"
":HP_Y+" ":HP_Y-" ":HP_E+" ":HP_E-"
hpMenuToUpdateFromChooser
java.lang.String hpMenuToUpdateFromChooser
- Set in event handler to one of: ":HP" ":HP_X" ":HP_Y" ":HP_X+" ":HP_X-"
":HP_Y+" ":HP_Y-" ":HP_E+" ":HP_E-"
hpMenuGuesser
PopupHPmenuGuesser hpMenuGuesser
- HP menu guesser: create when needed
projDirGuesser
PopupProjDirGuesser projDirGuesser
- Project Guesser: create when needed
projDirGuesserIsPoppedUp
boolean projDirGuesserIsPoppedUp
- if guesser was popped up
projDirToUpdateFromGuesser
java.lang.String projDirToUpdateFromGuesser
- prj dir result set in event handler
analysisMenu
java.awt.Menu analysisMenu
- "Analysis" menu
fileMenu
java.awt.Menu fileMenu
- "File" menu
sampleMenu
java.awt.Menu sampleMenu
- "Sample" command menu
geneClassMenu
java.awt.Menu geneClassMenu
- "GeneClass" menu
normMenu
java.awt.Menu normMenu
- "Normalization" menu
editMenu
java.awt.Menu editMenu
- "Edit" menu
filterMenu
java.awt.Menu filterMenu
- "Filter" menu
viewMenu
java.awt.Menu viewMenu
- "View" menu
plotMenu
java.awt.Menu plotMenu
- "Plot" menu
clusterMenu
java.awt.Menu clusterMenu
- "Cluster" menu
reportMenu
java.awt.Menu reportMenu
- "Report" menu
pluginsMenu
java.awt.Menu pluginsMenu
- "Plugins" menu
helpMenu
java.awt.Menu helpMenu
- "Help" menu
miFEMuseWebDB
java.awt.CheckboxMenuItem miFEMuseWebDB
- Menu: (Edit | Preferences) access data from Web database
miFEMenableFIOcache
java.awt.CheckboxMenuItem miFEMenableFIOcache
- Menu: (Edit | Preferences) enable using cache for Web database
miHPMuseHPxySets
java.awt.CheckboxMenuItem miHPMuseHPxySets
- Menu: (Samples) use HP-X and HP-Y 'sets' of multiple samples
else use individual HP-X and HP-Y samples.
miNRMhousekeepNorm
java.awt.CheckboxMenuItem miNRMhousekeepNorm
- (Analysis | Normalization | Housekeeping genes)
miNRMgeneSetNorm
java.awt.CheckboxMenuItem miNRMgeneSetNorm
- (Analysis | Normalization | User defined gene set genes)
miNRMCalDNAnorm
java.awt.CheckboxMenuItem miNRMCalDNAnorm
- (Analysis | Normalization | Calibration DNA genes)
miNRMZscoreNorm
java.awt.CheckboxMenuItem miNRMZscoreNorm
- (Analysis | Normalization | Zscore )
miNRMmedianNorm
java.awt.CheckboxMenuItem miNRMmedianNorm
- (Analysis | Normalization | Median)
miNRMlogMedianNorm
java.awt.CheckboxMenuItem miNRMlogMedianNorm
- (Analysis | Normalization | Normalize by logMedian )
miNRMZscoreMeanStdDevLogNorm
java.awt.CheckboxMenuItem miNRMZscoreMeanStdDevLogNorm
- (Analysis | Normalization | Normalize by Zscore of log (StdDev) )
miNRMZscoreMeanAbsDevLogNorm
java.awt.CheckboxMenuItem miNRMZscoreMeanAbsDevLogNorm
- (Analysis | Normalization | Normalize by Zscore of log (AbsDev) )
miNRMscaleToMaxIntens
java.awt.CheckboxMenuItem miNRMscaleToMaxIntens
- (Analysis | Normalization | Normalize to maximum intensity (65K)
miNRMnoNorm
java.awt.CheckboxMenuItem miNRMnoNorm
- (Analysis | Normalization } No normalization)
miNRMtestGenericNormPlugin
java.awt.CheckboxMenuItem miNRMtestGenericNormPlugin
- only if mae.DBUG_GENERIC_NORM_PLUGIN is set, then
(Analysis | Normalization | Test Generic Norm Plugin)
miNRMgoodSpotsStats
java.awt.CheckboxMenuItem miNRMgoodSpotsStats
- (Analysis | Normalization) use per-sample Good Spots data for
global array statistics
miNRMbkgrdCorr
java.awt.CheckboxMenuItem miNRMbkgrdCorr
- (Analysis | Normalization) use background correction
miNRMratioMedianCorrection
java.awt.CheckboxMenuItem miNRMratioMedianCorrection
- (Analysis | Normalization) use ratio median correction
for the Cy3 and Cy5 channels
miEMshowEditedGenes
java.awt.CheckboxMenuItem miEMshowEditedGenes
- Menu: (Edit | User Edited Gene List') Show 'Edited Gene List'
miEMeditNop
java.awt.CheckboxMenuItem miEMeditNop
- Menu: (Edit | User Edited Gene List') don't edit 'Edited Gene List'
miEMeditAdd
java.awt.CheckboxMenuItem miEMeditAdd
- Menu: (Edit | User Edited Gene List') add gene to 'Edited Gene List'
miEMeditRmv
java.awt.CheckboxMenuItem miEMeditRmv
- Menu: (Edit | User Edited Gene List') delete gene to 'Edited Gene List'
miEMautoScrollerPopup
java.awt.CheckboxMenuItem miEMautoScrollerPopup
- Menu: (Edit | User Edited Gene List') [DEPRICATED]
miEMclusterWorkingCL
java.awt.CheckboxMenuItem miEMclusterWorkingCL
- Menu: (Edit | Preferences) Cluster Filtered Genes, else all genes
miVMshowEditedGenes
java.awt.CheckboxMenuItem miVMshowEditedGenes
- Menu:(View) show EGL genes
miVMshowFilteredSpots
java.awt.CheckboxMenuItem miVMshowFilteredSpots
- Menu:(View) show Filtered genes and spots
miVMPresentView
java.awt.CheckboxMenuItem miVMPresentView
- Menu:(View) enable Presentation view that increases font sizes
miVMGang
java.awt.CheckboxMenuItem miVMGang
- Menu:(View) show gang scrolling for duplicated grids of spots
miVMuseMouseOver
java.awt.CheckboxMenuItem miVMuseMouseOver
- Menu:(View) enable mouse-over information for mouse over selected genes
miVMgenBankViewer
java.awt.CheckboxMenuItem miVMgenBankViewer
- Menu:(View) enable popup GenBank browser for new current gene
miVMdbESTviewer
java.awt.CheckboxMenuItem miVMdbESTviewer
- Menu:(View) enable popup GenBank browser for new current gene
miVMuniGeneViewer
java.awt.CheckboxMenuItem miVMuniGeneViewer
- Menu:(View) enable popup UniGene browser for new current gene
miVMomimViewer
java.awt.CheckboxMenuItem miVMomimViewer
- Menu:(View) enable popup OMIM browser for new current gene
miVMmAdbViewer
java.awt.CheckboxMenuItem miVMmAdbViewer
- Menu:(View) enable popup mAdb gene browser for new current gene
miVMlocusLinkViewer
java.awt.CheckboxMenuItem miVMlocusLinkViewer
- Menu:(View) enable popup LocusLink gene browser for new current gene
miVMmedMinerViewer
java.awt.CheckboxMenuItem miVMmedMinerViewer
- Menu:(View) enable popup MedMiner browser for new current gene
miVMswissProtViewer
java.awt.CheckboxMenuItem miVMswissProtViewer
- Menu:(View) enable popup SwissProt browser for new current gene
miVMpirViewer
java.awt.CheckboxMenuItem miVMpirViewer
- Menu:(View) enable popup PIRs browser for new current gene
miVMuseDichromasy
java.awt.CheckboxMenuItem miVMuseDichromasy
- Menu:(View) enable Dichromasy colors that may be useful for some
colorblind researchers instead of default color schemes.
miVMshowMsgLog
java.awt.CheckboxMenuItem miVMshowMsgLog
- Menu:(View) enable popup message history log
miVMshowHistoryLog
java.awt.CheckboxMenuItem miVMshowHistoryLog
- Menu:(View) enable popup command history log
miVMgenomicViewer
java.awt.CheckboxMenuItem[] miVMgenomicViewer
- sGenomicMenu[cfg.nGenomicMenus] menu items as determined from Config DB
miFRMgeneClassMbrFilter
java.awt.CheckboxMenuItem miFRMgeneClassMbrFilter
- Menu: (Analysis | Filter) Filter by GeneClass membership
miFRMuseGeneSetFilter
java.awt.CheckboxMenuItem miFRMuseGeneSetFilter
- Menu: (Analysis | Filter) Filter by user gene set membership
miFRMgoodGeneListFilter
java.awt.CheckboxMenuItem miFRMgoodGeneListFilter
- Menu: (Analysis | Filter) Filter by good genes membership
miFRMreplicateGenesFilter
java.awt.CheckboxMenuItem miFRMreplicateGenesFilter
- Menu: (Analysis | Filter) Filter by replicate genes membership
miFRMhistRatioRngFilter
java.awt.CheckboxMenuItem miFRMhistRatioRngFilter
- Menu: (Analysis | Filter) Filter by ratio histogram bin
miFRMhistIntensRngFilter
java.awt.CheckboxMenuItem miFRMhistIntensRngFilter
- Menu: (Analysis | Filter) Filter by intensity histogram bin
miFRM_EGLfilter
java.awt.CheckboxMenuItem miFRM_EGLfilter
- Menu: (Analysis | Filter) Filter by EGL gene membership
miFRMspotCVfilter
java.awt.CheckboxMenuItem miFRMspotCVfilter
- Menu: (Analysis | Filter) Filter by spot CV test
miFRMclusterHP_Efilter
java.awt.CheckboxMenuItem miFRMclusterHP_Efilter
- Menu: (Analysis | Filter) Filter by Cluster test
miFRMuseDiffFilter
java.awt.CheckboxMenuItem miFRMuseDiffFilter
- Menu: (Analysis | Filter) Filter by difference test
miFRMtTestXYfilter
java.awt.CheckboxMenuItem miFRMtTestXYfilter
- Menu: (Analysis | Filter) Filter by HP-X and HP-Y F1+F2 t-Test
miFRMtTestXYsetsFilter
java.awt.CheckboxMenuItem miFRMtTestXYsetsFilter
- Menu: (Analysis | Filter) Filter by HP-X and HP-Y 'sets' t-Test
miFRMksTestXYsetsFilter
java.awt.CheckboxMenuItem miFRMksTestXYsetsFilter
- Menu: (Analysis | Filter) Filter by HP-X and HP-Y 'sets' KS-Test
miFRMfTestOCLFilter
java.awt.CheckboxMenuItem miFRMfTestOCLFilter
- Menu: (Analysis | Filter) Filter by cur. OCL F-Test)
miFRMhighXYratioFilter
java.awt.CheckboxMenuItem miFRMhighXYratioFilter
- Menu: (Analysis | Filter) Filter by high ratio range test
miFRMlowXYratioFilter
java.awt.CheckboxMenuItem miFRMlowXYratioFilter
- Menu: (Analysis | Filter) Filter by low ratio range test
miFRMthrSpotIntens
java.awt.CheckboxMenuItem miFRMthrSpotIntens
- Menu: (Analysis | Filter | Filter by spot intensity [SI1:SI2] sliders)
Filter by spot intensity range test
miFRMspotIntensRngIn
java.awt.CheckboxMenuItem miFRMspotIntensRngIn
- Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders)
within range test
miFRMspotIntensRngOut
java.awt.CheckboxMenuItem miFRMspotIntensRngOut
- Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders)
outside range test
miFRMspotIntensModeMS
java.awt.CheckboxMenuItem miFRMspotIntensModeMS
- Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders)
test current HP sample
miFRMspotIntensModeXY
java.awt.CheckboxMenuItem miFRMspotIntensModeXY
- Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders)
test current HP-X and HP-Y samples
miFRMspotIntensModeXsets
java.awt.CheckboxMenuItem miFRMspotIntensModeXsets
- Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders)
test current HP-X 'sets' samples
miFRMspotIntensModeYsets
java.awt.CheckboxMenuItem miFRMspotIntensModeYsets
- Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders)
test current HP-Y 'sets' samples
miFRMspotIntensModeXORYsets
java.awt.CheckboxMenuItem miFRMspotIntensModeXORYsets
- Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders)
test current HP-X or HP-Y 'sets' samples
miFRMspotIntensModeXANDYsets
java.awt.CheckboxMenuItem miFRMspotIntensModeXANDYsets
- Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders)
test current HP-X and HP-Y 'sets' samples
miFRMspotIntensModeE
java.awt.CheckboxMenuItem miFRMspotIntensModeE
- Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders)
test current HP-E 'list' samples
miFRMspotIntensCompareModeALL
java.awt.CheckboxMenuItem miFRMspotIntensCompareModeALL
- Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders)
must have ALL selected samples
miFRMspotIntensCompareModeANY
java.awt.CheckboxMenuItem miFRMspotIntensCompareModeANY
- Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders)
must have ANY selected samples
miFRMspotIntensCompareModeAT_MOST
java.awt.CheckboxMenuItem miFRMspotIntensCompareModeAT_MOST
- Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders)
must have AT MOST (n) selected samples
miFRMspotIntensCompareModeAT_LEAST
java.awt.CheckboxMenuItem miFRMspotIntensCompareModeAT_LEAST
- Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders)
must have AT LEAST (n) selected samples
miFRMspotIntensCompareModePRODUCT
java.awt.CheckboxMenuItem miFRMspotIntensCompareModePRODUCT
- Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders)
must have PRODUCT selected samples less than threshold
miFRMspotIntensCompareModeSUM
java.awt.CheckboxMenuItem miFRMspotIntensCompareModeSUM
- Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders)
must have SUM selected samples less than threshold
miFRMthrGray
java.awt.CheckboxMenuItem miFRMthrGray
- Menu: (Analysis | Filter | by intensity range test)
enabled
miFRMgrayRngIn
java.awt.CheckboxMenuItem miFRMgrayRngIn
- Menu: (Analysis | Filter | by intensity range test)
within range
miFRMgrayRngOut
java.awt.CheckboxMenuItem miFRMgrayRngOut
- Menu: (Analysis | Filter | by intensity range test)
outside range
miFRMthrRatio
java.awt.CheckboxMenuItem miFRMthrRatio
- Menu: (Analysis | Filter | by ratio range test) enabled
miFRMratioRngIn
java.awt.CheckboxMenuItem miFRMratioRngIn
- Menu: (Analysis | Filter | by ratio range test) in range
miFRMratioRngOut
java.awt.CheckboxMenuItem miFRMratioRngOut
- Menu: (Analysis | Filter | Filter by ratio range test)
outside of range
miFRMthrCy3Cy5Ratio
java.awt.CheckboxMenuItem miFRMthrCy3Cy5Ratio
- Menu: (Analysis | Filter | Filter by Cy3/Cy5 ratio range test)
enabled
miFRMCy3Cy5RatioRngIn
java.awt.CheckboxMenuItem miFRMCy3Cy5RatioRngIn
- Menu: (Analysis | Filter | Filter by Cy3/Cy5 ratio range test)
in range
miFRMCy3Cy5RatioRngOut
java.awt.CheckboxMenuItem miFRMCy3Cy5RatioRngOut
- Menu: (Analysis | Filter | Filter by Cy3/Cy5 ratio range test)
outside of range
miFRMcvModeMS
java.awt.CheckboxMenuItem miFRMcvModeMS
- Menu: (Analysis | Filter | CV threshold sliders)
test current HP sample
miFRMcvModeXY
java.awt.CheckboxMenuItem miFRMcvModeXY
- Menu: (Analysis | Filter | CV threshold sliders)
test current HP sample
miFRMcvModeXset
java.awt.CheckboxMenuItem miFRMcvModeXset
- Menu: (Analysis | Filter | CV threshold sliders)
test current HP-X 'set' samples
miFRMcvModeYset
java.awt.CheckboxMenuItem miFRMcvModeYset
- Menu: (Analysis | Filter | CV threshold sliders)
test current HP-Y 'set' samples
miFRMcvModeXORYsets
java.awt.CheckboxMenuItem miFRMcvModeXORYsets
- Menu: (Analysis | Filter | CV threshold sliders)
test current HP-X or HP-Y 'sets' samples
miFRMcvModeXANDYsets
java.awt.CheckboxMenuItem miFRMcvModeXANDYsets
- Menu: (Analysis | Filter | CV threshold sliders)
test current HP-X and HP-Y 'sets' samples
miFRMcvModeE
java.awt.CheckboxMenuItem miFRMcvModeE
- Menu: (Analysis | Filter | CV threshold sliders)
test current HP sample
miFRMuseCVmeanElseMax
java.awt.CheckboxMenuItem miFRMuseCVmeanElseMax
- Menu: (Analysis | Filter | CV threshold sliders)
use the CV mean else the CV max in computation
miFRMusePosQuantDataFlag
java.awt.CheckboxMenuItem miFRMusePosQuantDataFlag
- Menu: (Analysis | Filter | use positive quantified data)
miFRMposQuantModeMS
java.awt.CheckboxMenuItem miFRMposQuantModeMS
- Menu: (Analysis | Filter | use positive quantified data)
test current HP sample
miFRMposQuantModeXY
java.awt.CheckboxMenuItem miFRMposQuantModeXY
- Menu: (Analysis | Filter | use positive quantified data)
test current HP-X and HP-Y samples
miFRMposQuantModeXYsets
java.awt.CheckboxMenuItem miFRMposQuantModeXYsets
- Menu: (Analysis | Filter | use positive quantified data)
test current HP-X and HP-Y 'set' samples
miFRMposQuantModeE
java.awt.CheckboxMenuItem miFRMposQuantModeE
- Menu: (Analysis | Filter | use positive quantified data)
test current HP-E 'list' samples
miFRMuseGoodSpotDataFlag
java.awt.CheckboxMenuItem miFRMuseGoodSpotDataFlag
- Menu: (Analysis | Filter | use Good Spot data)
miFRMgoodSpotModeMS
java.awt.CheckboxMenuItem miFRMgoodSpotModeMS
- Menu: (Analysis | Filter | use Good Spot data)
test current HP sample
miFRMgoodSpotModeXY
java.awt.CheckboxMenuItem miFRMgoodSpotModeXY
- Menu: (Analysis | Filter | use Good Spot data)
test current HP-X and HP-Y samples
miFRMgoodSpotModeXORYsets
java.awt.CheckboxMenuItem miFRMgoodSpotModeXORYsets
- Menu: (Analysis | Filter | use Good Spot data)
miFRMgoodSpotModeXANDYsets
java.awt.CheckboxMenuItem miFRMgoodSpotModeXANDYsets
- Menu: (Analysis | Filter | use Good Spot data)
test current HP-X and HP-Y 'set' samples
miFRMgoodSpotModeE
java.awt.CheckboxMenuItem miFRMgoodSpotModeE
- Menu: (Analysis | Filter | use Good Spot data)
test current HP-E 'list' samples
miFRMuseDetValueSpotDataFlag
java.awt.CheckboxMenuItem miFRMuseDetValueSpotDataFlag
- Menu: (Analysis | Filter | use Spot Detection Value data)
miFRMOnlyGenesWithNonZeroDensityFlag
java.awt.CheckboxMenuItem miFRMOnlyGenesWithNonZeroDensityFlag
- Menu: (Analysis | Filter | use only genes with non-zero intensity)
miFRMdetValueSpotModeMS
java.awt.CheckboxMenuItem miFRMdetValueSpotModeMS
- Menu: (Analysis | Filter | use Spot Detection Valuedata)
test current HP sample
miFRMdetValueSpotModeXY
java.awt.CheckboxMenuItem miFRMdetValueSpotModeXY
- Menu: (Analysis | Filter | use Spot Detection Value data)
test current HP-X and HP-Y samples
miFRMdetValueSpotModeXANDYsets
java.awt.CheckboxMenuItem miFRMdetValueSpotModeXANDYsets
- Menu: (Analysis | Filter | use Spot Detection Value data)
test current HP-X and HP-Y 'set' samples
miFRMdetValueSpotModeE
java.awt.CheckboxMenuItem miFRMdetValueSpotModeE
- Menu: (Analysis | Filter | use Spot Detection Value data)
test current HP-E 'list' samples
miPMplotPseudoImg
java.awt.CheckboxMenuItem miPMplotPseudoImg
- Menu:(Analysis | Plot | Show Microarray)
use Pseudograyscale intensity
miPMplotPseudoHP_XY_RYGImg
java.awt.CheckboxMenuItem miPMplotPseudoHP_XY_RYGImg
- Menu:(Analysis | Plot | Show Microarray)
use Pseudocolor Red(X)-Yellow-Green(Y) HP-X/Y ratio or Zdiff
miPMplotPseudoHP_F1F2_RYGImg
java.awt.CheckboxMenuItem miPMplotPseudoHP_F1F2_RYGImg
- Menu:(Analysis | Plot | Show Microarray)
use Pseudocolor Red(Cy5)-Yellow-Green(Cy3) Cy3/Cy5 ratio or Zdiff
miPMplotPseudoHP_XYImg
java.awt.CheckboxMenuItem miPMplotPseudoHP_XYImg
- Menu:(Analysis | Plot | Show Microarray)
use Pseudocolor HP-X/Y ratio or Zdiff
miPMplotPseudoF1F2Img
java.awt.CheckboxMenuItem miPMplotPseudoF1F2Img
- Menu:(Analysis | Plot | Show Microarray)
use Pseudocolor Cy3/Cy5 ratio or Zdiff
miPMplotPseudoHP_XY_pValueImg
java.awt.CheckboxMenuItem miPMplotPseudoHP_XY_pValueImg
- Menu:(Analysis | Plot | Show Microarray)
use Pseudocolor (HP-X,HP-Y) 'sets' p-value
miPMplotPseudoHP_EP_CV_valueImg
java.awt.CheckboxMenuItem miPMplotPseudoHP_EP_CV_valueImg
- Menu:(Analysis | Plot | Show Microarray)
use Pseudocolor HP-EP 'list' CV-value
miPMdualXYpseudoImg
java.awt.CheckboxMenuItem miPMdualXYpseudoImg
- Menu:(Analysis | Plot | Show Microarray)
use Pseudocolor dual HP-X and HP-Y as Field 1 and Field 2 grids
miPMflickerXY
java.awt.CheckboxMenuItem miPMflickerXY
- Menu:(Analysis | Plot | Show Microarray)
use Flicker of HP-X and HP-Y samples in intensity mode
miPMlowRangeZoom
java.awt.CheckboxMenuItem miPMlowRangeZoom
- Menu:(Analysis | Plot | Show Microarray)
use Pseudocolor low range zoom
miPEPlistType
java.awt.CheckboxMenuItem miPEPlistType
- (Analysis | Plot | Expression Profile) Menu
Expression Profile list type (overlay or grid).
miCLMfindSimGenesDisp
java.awt.CheckboxMenuItem miCLMfindSimGenesDisp
- Menu: (Analysis | Cluster) cluster by finding similar genes
miCLMsimGeneCountsDisp
java.awt.CheckboxMenuItem miCLMsimGeneCountsDisp
- Menu: (Analysis | Cluster) cluster by finding similar gene counts
miCLMhierClusterDisp
java.awt.CheckboxMenuItem miCLMhierClusterDisp
- Menu: (Analysis | Cluster) cluster by hierarchical clustering
miCLMdispKmeansNodes
java.awt.CheckboxMenuItem miCLMdispKmeansNodes
- Menu: (Analysis | Cluster) cluster by K-means
miCLMuseMedianKmeans
java.awt.CheckboxMenuItem miCLMuseMedianKmeans
- Menu: (Analysis | Cluster | cluster by K-means)
cluster using K-medians else use K-means
miCLMuseCorrCoeffDist
java.awt.CheckboxMenuItem miCLMuseCorrCoeffDist
- Menu: (Analysis | Cluster)
cluster using correlation coefficient else Euclidean distance
miCLMuseLSQmagNorm
java.awt.CheckboxMenuItem miCLMuseLSQmagNorm
- Menu: (Analysis | Cluster | hierarchical )
cluster using LSQ magnitude normalization else ...
miCLHCMavgPGMALnk
java.awt.CheckboxMenuItem miCLHCMavgPGMALnk
- Menu: (Analysis | Cluster | Hierarchical) use
average-arithmetic linkage for hier.clustering
miCLHCMavgPGMCLnk
java.awt.CheckboxMenuItem miCLHCMavgPGMCLnk
- Menu: (Analysis | Cluster | Hierarchical)
average-centroid linkage for hier.clustering
miCLHCMnextMinLnk
java.awt.CheckboxMenuItem miCLHCMnextMinLnk
- Menu: (Analysis | Cluster | Hierarchical)
next-min for linkage hier.clustering
miCLHCMunWtAvg
java.awt.CheckboxMenuItem miCLHCMunWtAvg
- Menu: (Analysis | Cluster | Hierarchical)
unweighted/weighted average for hier.clustering
miCLMnormHP
java.awt.CheckboxMenuItem miCLMnormHP
- Menu: (Analysis | Cluster | Hierarchical)
normalize EP by HP sample for hier.clustering
miCLHCMuseClusterDistCache
java.awt.CheckboxMenuItem miCLHCMuseClusterDistCache
- Menu: (Analysis | Cluster | Hierarchical)
use Cluster dist-dist cache matrix for hier.clustering
miCLHCMuseShortClusterDistCache
java.awt.CheckboxMenuItem miCLHCMuseShortClusterDistCache
- Menu: (Analysis | Cluster | Hierarchical)
use 16-bit short vs 32-bit float for hier.clustering
miTMtblFontSize8pt
java.awt.CheckboxMenuItem miTMtblFontSize8pt
- Menu: (Analysis | Report) font size is 8 pt
miTMtblFontSize10pt
java.awt.CheckboxMenuItem miTMtblFontSize10pt
- Menu: (Analysis | Report) font size is 10 pt
miTMtblFontSize12pt
java.awt.CheckboxMenuItem miTMtblFontSize12pt
- Menu: (Analysis | Report) font size is 12 pt
miPRtblFontSize8pt
java.awt.CheckboxMenuItem miPRtblFontSize8pt
- Menu: (Analysis | Report) font size is 8 pt
miPRtblFontSize10pt
java.awt.CheckboxMenuItem miPRtblFontSize10pt
- Menu: (Analysis | Report) font size is 10 pt
miPRtblFontSize12pt
java.awt.CheckboxMenuItem miPRtblFontSize12pt
- Menu: (Analysis | Report) font size is 12 pt
miTMtblFmtTabDelim
java.awt.CheckboxMenuItem miTMtblFmtTabDelim
- Menu: (Analysis | Report) use Tab-Delimited table format
miTMtblFmtClickable
java.awt.CheckboxMenuItem miTMtblFmtClickable
- Menu: (Analysis | Report) use Dynamic clickable table format
miTMtblFmtAddEPdata
java.awt.CheckboxMenuItem miTMtblFmtAddEPdata
- Menu: (Analysis | Report) add Expr-Profile data to Table
miTMtblFmtUseRawEPdata
java.awt.CheckboxMenuItem miTMtblFmtUseRawEPdata
- Menu: (Analysis | Report) use raw Expr-Profile data in Table
miTMtblFmtAddHP_XYsetStat
java.awt.CheckboxMenuItem miTMtblFmtAddHP_XYsetStat
- Menu: (Analysis | Report) add HP-XY set statistics data to Table
miTMtblFmtAddOCLstatistics
java.awt.CheckboxMenuItem miTMtblFmtAddOCLstatistics
- Menu: (Analysis | Report) add OCL statistics data to Table
miPLGMuseSPLUSasComputingEngine
java.awt.CheckboxMenuItem miPLGMuseSPLUSasComputingEngine
- Menu: (Plugins | Use S-PLUS, else R, as computing engine [CB])
miPLGMuseTimeStampReports
java.awt.CheckboxMenuItem miPLGMuseTimeStampReports
- Menu: (Plugins | Save SRLO reports in time-stampled folder [CB])
HP_Xlabel
java.awt.Label HP_Xlabel
- GUI label for current HP-X
HP_Ylabel
java.awt.Label HP_Ylabel
- GUI label for current HP-Y
mae
MAExplorer mae
- link to MAExplorer instance
data1
java.lang.String data1
- for returning data back to MAE
data2
java.lang.String data2
- for returning data back to MAE
data3
java.lang.String data3
- for returning data back to MAE
colSize
int colSize
- # of columns to display
width
int width
- size of frame
height
int height
- size of frame
frame
java.awt.Frame frame
- popup frame instance
optionPanel1
java.awt.Panel optionPanel1
- panel that holds choice list
optionPanel2
java.awt.Panel optionPanel2
- panel that holds choice list
optionPanel3
java.awt.Panel optionPanel3
- panel that holds choice list
optionChoice1
java.awt.Choice optionChoice1
- opt. option choice list
optionChoice2
java.awt.Choice optionChoice2
- opt. option choice list
optionChoice3
java.awt.Choice optionChoice3
- opt. option choice list
textField1
java.awt.TextField textField1
- place text to be edited here
textField2
java.awt.TextField textField2
- place text to be edited here
textField3
java.awt.TextField textField3
- place text to be edited here
label1
java.awt.Label label1
- for data label
label2
java.awt.Label label2
- for data label
label3
java.awt.Label label3
- for data label
sleepFlag
boolean sleepFlag
- wait for button to be pushed
listener
java.awt.event.ActionListener listener
- Tried this instead of "this"
spaces
java.lang.String spaces
- spaces
optionValues
java.lang.String[] optionValues
- list of option values if present
nOptions
int nOptions
- optionValues[0:nOptions]
mjaCondition
MJAcondition mjaCondition
- MaeJavaAPI classes
mjaFilter
MJAfilter mjaFilter
mjaProperty
MJAproperty mjaProperty
mjaReport
MJAreport mjaReport
mjaUtil
MJAutil mjaUtil
mjaSample
MJAsample mjaSample
addCondButton
java.awt.Button addCondButton
- Add condition
removeCondButton
java.awt.Button removeCondButton
- remove condition
listCondButton
java.awt.Button listCondButton
- list condition
listAllCondButton
java.awt.Button listAllCondButton
- list all condition
addParamButton
java.awt.Button addParamButton
- add condition parameter
rmvParamButton
java.awt.Button rmvParamButton
- remove condition parameter
saveButton
java.awt.Button saveButton
- save
doneButton
java.awt.Button doneButton
- done
cancelButton
java.awt.Button cancelButton
- cancel
pccgWidth
int pccgWidth
- size for PopupCondChooserGUI
pccgHeight
int pccgHeight
- size for PopupCondChooserGUI
preferredHeight
int preferredHeight
- preferred height size of frame
preferredWidth
int preferredWidth
- preferred width size of frame
fontFamily
java.lang.String fontFamily
- Font family from MAExplorer - using mjaProperty.getReportFontFamily()
dataFont
java.awt.Font dataFont
- font for data used in the Chooser GUI
buttonFont
java.awt.Font buttonFont
- font for buttons
labelFont
java.awt.Font labelFont
- font for labels
titleFont
java.awt.Font titleFont
- font for labels
msgFont
java.awt.Font msgFont
- font for title at the top of the main window
paramFont
java.awt.Font paramFont
- font for parameter Name and Value
condFont
java.awt.Font condFont
- font for conditions
msgTF
java.awt.TextField msgTF
- Text message report line
msgColor
java.awt.Color msgColor
- Text message foreground color that may be changed
msgBkgrd
java.awt.Color msgBkgrd
- Text message background color that may be changed
dataColor
java.awt.Color dataColor
- Text data report foreground color that may be changed
dataBkgrd
java.awt.Color dataBkgrd
- Text data report background color that may be changed
condList
java.awt.List condList
- The working list of conditions for GUI
chooserPanel
java.awt.Panel chooserPanel
- Panel for condition data
condPanel
java.awt.Panel condPanel
- Panel to hold conditions list (LEFT) and Param Editor (RIGHT)
pccMsgTxtField1
java.awt.TextField pccMsgTxtField1
- msg display 1
pccMsgTxtField2
java.awt.TextField pccMsgTxtField2
- msg display 2
pccMsgTxtField3
java.awt.TextField pccMsgTxtField3
- msg display 3
condErrorMsgTf
java.awt.TextField condErrorMsgTf
- error msg display
banner
java.lang.String banner
- Title banner for the main window
cd
PopupCondChooser.CondData[] cd
- List [0:maxPossibleCond-1] of working condition
data: name, selected and remainder samples,
param form (name,value).
nbrCondLists
int nbrCondLists
- number of condition lists
cpef
PopupCondChooser.CondParamEditForm cpef
- CondParamEditForm instance
curCond
java.lang.String curCond
- The current condition name
paramNames
java.lang.String[] paramNames
- list [0:nbrCondLists-1] of condition parameter names for
CondParamEditForm.
nbrParams
int nbrParams
- # of condition parameters
saveReportAsTextFileFlag
boolean saveReportAsTextFileFlag
- Flag enabled if doing "SaveAs"
saveFlag
boolean saveFlag
- see if saved ok
valueChangedFlag
boolean valueChangedFlag
- if something is changed, need to save it so keep track
remTitle
java.lang.String remTitle
- title of remainder samples TextArea for PopupCondChooserGUI
selTitle
java.lang.String selTitle
- title of selected samples TextArea for PopupCondChooserGUI
prevCPEFidx
int prevCPEFidx
- previous CondParamEditForm index
curCondIdx
int curCondIdx
- current cond index
condListNames
java.lang.String[] condListNames
- list of condition names
curCondNameLabel
java.awt.Label curCondNameLabel
- show current condition name
curCondListName
java.lang.String curCondListName
- show current condition name
maxNbrSamples
int maxNbrSamples
- Maximum # of samples currently in the database. This is the largest
size (in # samples) a condition list can be.
allSampleNames
java.lang.String[] allSampleNames
- list of ALL samples in the database
remSamplesTmp
java.lang.String[] remSamplesTmp
- remaining sample names of condition before edit
selSamplesTmp
java.lang.String[] selSamplesTmp
- selected sample names of condition before edit
pccgSample
PopupCondChooserGUI pccgSample
- chooser GUI for sample data
oldPccgSample
PopupCondChooserGUI oldPccgSample
- previous chooser GUI for sample data
this$0
PopupCondChooser this$0
pcc
PopupCondChooser pcc
- instance of PopupCondChooser
f
java.awt.Frame f
- pass down frame for dialog
selectedIndex
int selectedIndex
- index of which item is selected. Note: the first [0] item is used for initalMsg on selection
returnItem
java.lang.String returnItem
- return selected item when done button is pressed after remove button is pressed
removeMsg
java.lang.String removeMsg
- specific msg to be displayed about what is being removed interface parameter or condition
initialMsg
java.lang.String initialMsg
- in the list at position 0, first thing the user will see
choiceStr
java.lang.String choiceStr
- item in list that was clicked on by user
choiceList
java.awt.Choice choiceList
- list of items to select from
removeFlag
boolean removeFlag
- if selection went ok
cancelButton
java.awt.Button cancelButton
- cancel w/o removing
removeButton
java.awt.Button removeButton
- remove
doneButton
java.awt.Button doneButton
- Done button
this$0
PopupCondChooser this$0
f
java.awt.Frame f
- Frame where dialog box is added
msg
java.lang.String msg
- Message for dialog box
yesMsg
java.lang.String yesMsg
- Yes label for dialog box
noMsg
java.lang.String noMsg
- No label for dialog box
okFlag
boolean okFlag
- flag from OK button
this$0
PopupCondChooser this$0
pcc
PopupCondChooser pcc
- parent class
cd
PopupCondChooser.CondData cd
- instance of condData
bl
java.awt.BorderLayout bl
- main layout
labelGL
java.awt.GridLayout labelGL
- labels GridLayout to create condition form
tfGL
java.awt.GridLayout tfGL
- TextFields GridLayout to create condition form
labelPanel
java.awt.Panel labelPanel
- labels go here
tfPanel
java.awt.Panel tfPanel
- TextFields go here
mainPanel
java.awt.Panel mainPanel
- place both labelPanel & tfPanel to create form
nameTF
java.awt.TextField[] nameTF
- parameter names fields
valueChangedFlag
boolean valueChangedFlag
- a value was changed for THIS condition in one or more parametes, so
data will need to be saved.
nParams
int nParams
this$0
PopupCondChooser this$0
pcc
PopupCondChooser pcc
- instance of PopupCondChooser
newNameTF
java.awt.TextField newNameTF
- textfield for typing in new name
cancelButton
java.awt.Button cancelButton
- cancel button
doneButton
java.awt.Button doneButton
- done button
stringValidFlag
boolean stringValidFlag
- This is set if the name the user types is valid
newString
java.lang.String newString
- used to return the string the user types in
cc
PopupCondChooser cc
- instance of PopupCondChooser
id
int id
- id # for this instance
maxHybSamples
int maxHybSamples
- the MAX # of samples is specified by MAExplorer
addChangePosFlag
boolean addChangePosFlag
- if can move SELECTED entry up/down
remoteFlag
boolean remoteFlag
- true if using other prj data/ta
isWinPCflag
boolean isWinPCflag
- The system is a windows PC
valueChangedFlag
boolean valueChangedFlag
- value changed
remainderMeh
PopupCondChooserGUI.MouseEventHandler remainderMeh
- handle mouse events for text areas for remTextArea LEFT
selectMeh
PopupCondChooserGUI.MouseEventHandler selectMeh
- handle mouse events for text areas for selTextArea RIGHT
remTextArea
java.awt.TextArea remTextArea
- REMAINDER objs
selTextArea
java.awt.TextArea selTextArea
- SELECTED obj list
addButton
java.awt.Button addButton
- Move the Remainder entry to Selected
delButton
java.awt.Button delButton
- Nove the Selected entry to Remainder
addAllButton
java.awt.Button addAllButton
- Move ALL Remainder entries to Selected
rmvAllButton
java.awt.Button rmvAllButton
- Move ALL Selected entries to Remainder
upButton
java.awt.Button upButton
- Move SELECTED entry up if possible
downButton
java.awt.Button downButton
- Move SELECTED entry down if possible
controlPanel
java.awt.Panel controlPanel
- control panel for main ok/reset buttons
buttonPanel
java.awt.Panel buttonPanel
- buttons panel
prjListPanel
java.awt.Panel prjListPanel
- project prj ta
objButtonPanel
java.awt.Panel objButtonPanel
- set prj button
objListTApanel
java.awt.Panel objListTApanel
- obj list remTextArea
upDownPanel
java.awt.Panel upDownPanel
- panel with up/down buttons
addDelAllButtonPanel
java.awt.Panel addDelAllButtonPanel
- add,del,all buttons
selectedPanel
java.awt.Panel selectedPanel
- SELECTED list
changePosPanel
java.awt.Panel changePosPanel
- change up/down position panel
remTextAreaLabel
java.awt.Label remTextAreaLabel
- label under remTextArea
selTextAreaLabel
java.awt.Label selTextAreaLabel
- label under selTextArea
useAbove
java.awt.Label useAbove
- optional label if not to use remTextArea from above
lTitle
java.awt.Label lTitle
- label for title for entire GUI window
taRows
int taRows
- rows/text area
taCols
int taCols
- columns/text area
origRemObjsSize
int origRemObjsSize
- REMAINDER list size
origSelObjsSize
int origSelObjsSize
- SELECTED list size
remObjListSize
int remObjListSize
- REMAINDER list size
selObjListSize
int selObjListSize
- SELECTED list size
title
java.lang.String title
- title for entire GUI window
remLabelName
java.lang.String remLabelName
- label for SELECTED LEFT text area
selLabelName
java.lang.String selLabelName
- label for REMAINDER RIGHT text area
origRemObjs
java.lang.String[] origRemObjs
- original REMAINDER list
origSelObjs
java.lang.String[] origSelObjs
- original SELECTED list
remObjList
java.lang.String[] remObjList
- REMAINDER list of sample objects, returned if needed
selObjList
java.lang.String[] selObjList
- SELECTED list of sample object names to be returned
ccGUI
PopupCondChooserGUI ccGUI
- This is either the remote instance or 'this' instance of PopupCondChooserGUI
for the instance of REMAINDER to use.
titleFont
java.awt.Font titleFont
- font used by title
labelFont
java.awt.Font labelFont
- font used by label
dataFont
java.awt.Font dataFont
- font used by data
buttonFont
java.awt.Font buttonFont
- button font
ccGUIpanel
java.awt.Panel ccGUIpanel
- main GUI panel
parentWindow
java.lang.Object parentWindow
- parent window
mae
MAExplorer mae
- link to global instance to MAExplorer
data
java.lang.String data
- for returning data back to MAE
colSize
int colSize
- # of columns to display
width
int width
- size of frame
height
int height
- size of frame
frame
java.awt.Frame frame
- popup frame instance
textField
java.awt.TextField textField
- place text to be edited here
label
java.awt.Label label
- for data label
optionPanel
java.awt.Panel optionPanel
- for options
optionChoice
java.awt.Choice optionChoice
- opt. option choice list
addButtonsCnt
int addButtonsCnt
- # of buttons to add.
if 0, then none,
if 1, then add CONTINUE,
if 2 then add OK and CANCEL.
alertDone
boolean alertDone
- button pressed flag
sleepFlag
boolean sleepFlag
- wait for button to be pushed
listener
java.awt.event.ActionListener listener
- Tried this instead of "this"
spaces
java.lang.String spaces
- DEF_COL_SIZE spaces
optionValues
java.lang.String[] optionValues
- list of option values if present
nOptions
int nOptions
- optionValues[0:nOptions]
rtb
RtestBase rtb
- instance of the parent
mr
MJAReval mr
- short form instance of mjaReval
mjaUtil
MJAutil mjaUtil
rgd
RgenDemo rgd
- R demo code generator
preferredHeight
int preferredHeight
- preferred height size of frame
preferredWidth
int preferredWidth
- preferred width size of frame
editingRLOflag
boolean editingRLOflag
- Flag set if editing a RLO
editRscriptTextArea
java.awt.TextArea editRscriptTextArea
- Text area to draw editRscriptText in popup window.
msgTextField
java.awt.TextField msgTextField
- Text field to hold popup edit messages.
showHelpCheckbox
java.awt.Checkbox showHelpCheckbox
- Show Help message text box.
showHelpFlag
boolean showHelpFlag
- Flag to display help message
helpStr
java.lang.String helpStr
- The help message
topEditPanel
java.awt.Panel topEditPanel
centerPanel
java.awt.Panel centerPanel
- Center Panel to hold the text area and the wizard panel.
controlPanel
java.awt.Panel controlPanel
- Control Panel to hold buttons and GenR checkboxes in popup window.
editButtonsPanel
java.awt.Panel editButtonsPanel
- Control Panel to hold buttons in popup window.
mainWizardPanel
java.awt.Panel mainWizardPanel
- main wizard panel, separates top label from grid of TF and labels
wizardPanel
java.awt.Panel wizardPanel
- Wizard Panel
lastWizardNbr
int lastWizardNbr
mainWizardPanelLabel
java.awt.Label mainWizardPanelLabel
- main label for wizard panel
labelWizard
java.awt.Label[] labelWizard
- Wizard title labels [0:MAX_WIZ_ROWS-1]
textFieldWizard
java.awt.TextField[] textFieldWizard
- Wizard title text fields [0:MAX_WIZ_ROWS-1]
wizardChoice
java.awt.Choice wizardChoice
- Wizard choice widget
fullWizardList
int[] fullWizardList
- List of wizards for full Wizard of new RLOs
demoWizardList
int[] demoWizardList
- List of wizards for Demo Wizard of pre-constructed RLOs
wizardNames
java.lang.String[] wizardNames
- List of Wizard options
nWizards
int nWizards
- # of wizards
wizardNbr
int wizardNbr
- default wizard to use at startup index wizardNames[]
relWizardNbr
int relWizardNbr
- relative index through either fullWizardList[] or
demoWizardList[] to then access wizardNames[].
menuStubChoice
java.awt.Choice menuStubChoice
- menu stub choice widget
legalMenuStubNames
java.lang.String[] legalMenuStubNames
nMenuStubNames
int nMenuStubNames
- # of menu stub names
generateTemplateButton
java.awt.Button generateTemplateButton
- Generate R template code button
templateValue
int templateValue
- selected template value # from R_DATA_TYPE_xxxx
Note: this is the type of the 1st input file
importRfileButton
java.awt.Button importRfileButton
- "Import .R file"
saveRLOButton
java.awt.Button saveRLOButton
- "Save RLO" window button
prevButton
java.awt.Button prevButton
- "Prev" wizard button
nextButton
java.awt.Button nextButton
- "Next" wizard button
cancelButton
java.awt.Button cancelButton
- "Cancel" window button
closeButton
java.awt.Button closeButton
- "Close" window button
rloTitleLabel
java.awt.Label rloTitleLabel
- title label
rloMenuNameLabel
java.awt.Label rloMenuNameLabel
- current RLO being edited
rloTitleMsg
java.lang.String rloTitleMsg
- RLO edit title label msg
rloMenuNameMsg
java.lang.String rloMenuNameMsg
- RLO edit menuName msg
inputTypesChoice
java.awt.Choice[] inputTypesChoice
- Input data type Choices [0:MAX_WIZ_CHOICES-1]
inputTypesChoiceNames
java.lang.String[] inputTypesChoiceNames
- Input data types Choice names [0:nInputTypes-1]
inputTypesChoiceValues
int[] inputTypesChoiceValues
- data types Choice values [0:nInputTypes-1]. All values >= 1
nInputTypesValues
int nInputTypesValues
- # of input data type values
outputTypesChoice
java.awt.Choice[] outputTypesChoice
- Output data type Choices [0:MAX_WIZ_CHOICES-1]
outputTypesChoiceNames
java.lang.String[] outputTypesChoiceNames
- Output data types Choice names [0:nOutputTypes-1]
outputTypesChoiceValues
int[] outputTypesChoiceValues
- Output data types Choice values [0:nOutputTypes-1]. All values >= 1
nOutputTypeValues
int nOutputTypeValues
- # of input data types
r2ClientActionChoice
java.awt.Choice[] r2ClientActionChoice
- R2Client action Choices [0:MAX_WIZ_CHOICES-1]
r2ClientActionChoiceNames
java.lang.String[] r2ClientActionChoiceNames
- R2Client action Choice names [0:nr2ClientActions-1]
R2ClientTypesChoiceValues
int[] R2ClientTypesChoiceValues
- R2Client action Choice values [0:nr2ClientActions-1]
nr2ClientActionValues
int nr2ClientActionValues
- # of R2Client action Choice values
processCheckbox
java.awt.Checkbox[] processCheckbox
- Process bits checkboxes [0:nProcessCB-1]
processCBname
java.lang.String[] processCBname
- Process checkbox names [0:nProcessCB-1]
processCBbits
int[] processCBbits
- Process checkbox processBits [0:nProcessCB-1] from R_PB_xxxx.
All values >= 1
nProcessCB
int nProcessCB
- # of Process checkbox entries
useGenRcheckbox
java.awt.Checkbox[] useGenRcheckbox
- Rscript generation GUI for DEMO only: add separate method generators
useGenRname
java.lang.String[] useGenRname
- Rscript generation GUI for DEMO only: add separate method generators
useGenRbit
int[] useGenRbit
- Rscript generation GUI for DEMO only: add separate method generators
nUseGenRCB
int nUseGenRCB
- Rscript generation GUI for DEMO only: # of entries
closeGenRButton
java.awt.Button closeGenRButton
- "Close" window button for DEMO GenR edit
isNewRLOflag
boolean isNewRLOflag
- Flag that indicates we are editing a new RLO or editing an old one
outsideLoadRscriptFile
java.lang.String outsideLoadRscriptFile
- outside Load .R script File
editedRscriptFile
java.lang.String editedRscriptFile
- edited Load .R script File
editRscriptText
java.lang.String editRscriptText
- .R text or help message
RscriptText
java.lang.String RscriptText
- .R text
rloID
int rloID
- sequence # of description
menuName
java.lang.String menuName
- Analysis menu name
menuStubName
java.lang.String menuStubName
- Desired Client menu stub. If null or "", then put in
(Plugins | RLO methods submenu)
RscriptName
java.lang.String RscriptName
- Name of .R script file
nInputFiles
int nInputFiles
- # of input files if any, 0 if none
inputDataFileNames
java.lang.String[] inputDataFileNames
- Name of input file if any (if not null)
inputDataTypes
int[] inputDataTypes
- R_DATA_TYPE_xxxx type of input file if any
processBits
int processBits
- Process Bits is a bit pattern of selected (R_PB_xxxx) options
used during processing
genRbits
int genRbits
- GenR Bits is a bit pattern of selected (R_GENR_xxxx) options
used during .R script generation.
nOutputFiles
int nOutputFiles
- # of output files if any, 0 if none
outputDataFileNames
java.lang.String[] outputDataFileNames
- List of output files if any, null if none
outputDataTypes
int[] outputDataTypes
- List of R_FILE_TYPE_xxxx types of output files if any,
null if none.
nSetR2ClientFiles
int nSetR2ClientFiles
- # of output files used to set R to client data if any, 0 if none
setR2ClientFileNames
java.lang.String[] setR2ClientFileNames
- List of output file names used to set R to client data if
any, null if none
setR2ClientObjNames
java.lang.String[] setR2ClientObjNames
- List of Client object names used to set R to client data if any,
null if none. E.g., If the object is a gene set (condition list),
then this is the gene set (condition list) name
setR2ClientObjTypes
int[] setR2ClientObjTypes
- List of R_SET_R2Client_xxxx types of output files if any,
null if none.
cursorLoc
int cursorLoc
- keep track of cursor location within textarea
scriptSpecificRoptions
java.lang.String scriptSpecificRoptions
- Optional script Specific R startup options. These can include
things like "--vsize=20M", or "--nsize=200k", etc. See
the R reference manual for specific options.
strDataIsSortedFlag
boolean strDataIsSortedFlag
- set once it is sorted
taRows
int taRows
- default size of text area
taCols
int taCols
- default size of text area
doubleListFlag
boolean doubleListFlag
- numeric/alpha or alpha only
mae
MAExplorer mae
- link to global MAExplorer instance
hps
SampleSets hps
- link to global SampleSets instance
id
int id
- id # for this instance
f
java.awt.Frame f
- frame to install choosers
frameWidth
int frameWidth
- default frame size - must be here!
frameHeight
int frameHeight
- default frame size - must be here!
cgIdx
int cgIdx
- index of chooser instance in cgList[]
taRows
int taRows
- TextArea rows dimensions
taCols
int taCols
- TextArea cols dimensions
nChooser
int nChooser
- number of ChooseGUI instances
cgList
ChooserGUI[] cgList
- [0:nChooser-1] list of chooserGUIs
nHPXo
int nHPXo
- # of original HP-X selected samples
nHPYo
int nHPYo
- # of original HP-Y selected samples
nHPEo
int nHPEo
- # of original HP-E selected samples
nHP
int nHP
- # all probes in the database
nHPrXY
int nHPrXY
- # rem(X+Y) = mxListo - msListXo - msListYo
nHPrE
int nHPrE
- # rem(E) = mxListo - msListEo
nHPXf
int nHPXf
- # of final selected HP-X samples
nHPYf
int nHPYf
- # of final selected HP-Y samples
nHPEf
int nHPEf
- # of final selected HP-E samples
hpMenuItemListSize
int hpMenuItemListSize
- sorted list of HP menu size
msListXo
MaHybridSample[] msListXo
- initial HP-X sample list on starting chooser
msListYo
MaHybridSample[] msListYo
- initial HP-Y sample list on starting chooser
msListEo
MaHybridSample[] msListEo
- initial HP-E sample list on starting chooser
msList
MaHybridSample[] msList
- List of ALL initial samples in DB
msListrXY
MaHybridSample[] msListrXY
- rem(X+Y) = mxListo - msListXo - msListYo
msListrE
MaHybridSample[] msListrE
- rem(E) = mxListo - msListEo
sListXo
java.lang.String[] sListXo
- initial HP-X sample list on starting chooser
sListYo
java.lang.String[] sListYo
- initial HP-Y sample list on starting chooser
sListEo
java.lang.String[] sListEo
- initial HP-E list on starting chooser
sList
java.lang.String[] sList
- List of ALL initial samples in DB
sListrXY
java.lang.String[] sListrXY
- rem(X+Y) = msListo - msListXo - msListYo
sListrE
java.lang.String[] sListrE
- rem(E) = msListo - msListEo
title
java.lang.String title
- title of popup chooser window
titleFont
java.awt.Font titleFont
- font for title of popup chooser window
labelFont
java.awt.Font labelFont
- font for labels of popup chooser window
dataFont
java.awt.Font dataFont
- font for data of popup chooser window
infoTA1
java.awt.TextField infoTA1
- first line of info about selected HP
infoTA2
java.awt.TextField infoTA2
- second line of info about selected HP
infoTA3
java.awt.TextField infoTA3
- third line of info about selected HP
taRows
int taRows
- default size of text area
taCols
int taCols
- default size of text area
mae
MAExplorer mae
- link to global instance of MAExplorer
defaultMsg
java.lang.String defaultMsg
- default prompt string
optMsg
java.lang.String optMsg
- for optional message label
loginNameData
java.lang.String loginNameData
- login name to pass back to MAE
passwordData
java.lang.String passwordData
- password data for returning back to MAE
colSize
int colSize
- # of columns to use
width
int width
- size of frame
height
int height
- size of frame
frame
java.awt.Frame frame
loginTextField
java.awt.TextField loginTextField
- place login text to be edited here
passwordTextField
java.awt.TextField passwordTextField
- place password text to be edited here
optLabel
java.awt.Label optLabel
- for optional message label
loginLabel
java.awt.Label loginLabel
- for login label
passwordLabel
java.awt.Label passwordLabel
- for password label
dataOK
boolean dataOK
- flag set by OK and Cancel buttons
sleepFlag
boolean sleepFlag
- flag to wait for button to be pushed
listener
java.awt.event.ActionListener listener
spaces
java.lang.String spaces
- variable holding spaces
mjaCondition
MJAcondition mjaCondition
- MaeJavaAPI classes
mjaFilter
MJAfilter mjaFilter
mjaProperty
MJAproperty mjaProperty
mjaReport
MJAreport mjaReport
mjaUtil
MJAutil mjaUtil
addOCLButton
java.awt.Button addOCLButton
- add ordered cond list
removeOCLButton
java.awt.Button removeOCLButton
- remove order cond list
listOCLButton
java.awt.Button listOCLButton
- list order cond
listAllButton
java.awt.Button listAllButton
- list all ordered cond lists
addAnnButton
java.awt.Button addAnnButton
- add annotation
rmvAnnButton
java.awt.Button rmvAnnButton
- remove annotation
saveButton
java.awt.Button saveButton
- save to MAExplorer
doneButton
java.awt.Button doneButton
- done
cancelButton
java.awt.Button cancelButton
- cancel
pccgWidth
int pccgWidth
- size for PopupOrderedCondChooserGUI
pccgHeight
int pccgHeight
- size for PopupOrderedCondChooserGUI
preferredHeight
int preferredHeight
- preferred height size of frame
preferredWidth
int preferredWidth
- preferred width size of frame
fontFamily
java.lang.String fontFamily
- Font family from MAExplorer - using mjaProperty.getReportFontFamily()
dataFont
java.awt.Font dataFont
- font for data used in the Chooser GUI
buttonFont
java.awt.Font buttonFont
- font for buttons
labelFont
java.awt.Font labelFont
- font for labels
titleFont
java.awt.Font titleFont
- font for labels
msgFont
java.awt.Font msgFont
- font for title at the top of the main window
paramFont
java.awt.Font paramFont
- font for parameter Name and Value
condFont
java.awt.Font condFont
- font for conditions
msgTF
java.awt.TextField msgTF
- Text message report line
msgColor
java.awt.Color msgColor
- Text message foreground color that may be changed
msgBkgrd
java.awt.Color msgBkgrd
- Text message background color that may be changed
dataColor
java.awt.Color dataColor
- Text data report foreground color that may be changed
dataBkgrd
java.awt.Color dataBkgrd
- Text data report background color that may be changed
oclList
java.awt.List oclList
- The working list of conditions for GUI
chooserPanel
java.awt.Panel chooserPanel
- Panel for condition data
oclPanel
java.awt.Panel oclPanel
- Panel to hold conditions list (LEFT) and Param Editor (RIGHT)
pccMsgTxtField1
java.awt.TextField pccMsgTxtField1
- msg display 1
pccMsgTxtField2
java.awt.TextField pccMsgTxtField2
- msg display 2
pccMsgTxtField3
java.awt.TextField pccMsgTxtField3
- msg display 3
condErrorMsgTf
java.awt.TextField condErrorMsgTf
- error msg display
banner
java.lang.String banner
- Title banner for the main window
oclLd
PopupOrderedCondChooser.OclListData[] oclLd
- List [0:maxPossibleCond-1] of working condition
data: name, selected and remainder cond,
param form (name,value).
nbrOclLists
int nbrOclLists
- number of condition lists
cpef
PopupOrderedCondChooser.CondParamEditForm cpef
- CondParamEditForm instance
curCond
java.lang.String curCond
- The current condition name that is selected in the lower OCL list
curCondNames
java.lang.String[] curCondNames
- The current condition list of names
paramNames
java.lang.String[] paramNames
- list [0:nbrOclLists-1] of condition parameter names for
CondParamEditForm.
nbrParams
int nbrParams
- # of condition parameters
saveReportAsTextFileFlag
boolean saveReportAsTextFileFlag
- Flag enabled if doing "SaveAs"
saveFlag
boolean saveFlag
- see if saved ok
valueChangedFlag
boolean valueChangedFlag
- if something is changed, need to save it so keep track
remTitle
java.lang.String remTitle
- title of remainder TextArea for PopupOrderedCondChooserGUI
selTitle
java.lang.String selTitle
- title of selected TextArea for PopupOrderedCondChooserGUI
prevCPEFidx
int prevCPEFidx
- previous CondParamEditForm index
curCondIdx
int curCondIdx
- current cond index
allConditionNames
java.lang.String[] allConditionNames
- list of all condition names
orderedCondListNames
java.lang.String[] orderedCondListNames
- list of condition names
curOclNameLabel
java.awt.Label curOclNameLabel
- show current condition name
curOclListName
java.lang.String curOclListName
- show current condition name
maxNbrCond
int maxNbrCond
- Maximum # of Conditions currently in the database. This is the largest
size (in # Conditions) a condition list can be.
remCondTmp
java.lang.String[] remCondTmp
- remaining conditions before edit
selCondTmp
java.lang.String[] selCondTmp
- selected conditions before edit
pccg
PopupOrderedCondChooserGUI pccg
- Ordered chooser GUI for cond data
oldPccg
PopupOrderedCondChooserGUI oldPccg
- previous chooser GUI for cond data
this$0
PopupOrderedCondChooser this$0
pcc
PopupOrderedCondChooser pcc
- instance of PopupOrderedCondChooser
f
java.awt.Frame f
- pass down frame for dialog
selectedIndex
int selectedIndex
- index of which item is selected. Note: the first [0] item is used for initalMsg on selection
returnItem
java.lang.String returnItem
- return selected item when done button is pressed after remove button is pressed
removeMsg
java.lang.String removeMsg
- specific msg to be displayed about what is being removed interface parameter or condition
initialMsg
java.lang.String initialMsg
- in the list at position 0, first thing the user will see
choiceStr
java.lang.String choiceStr
- item in list that was clicked on by user
choiceList
java.awt.Choice choiceList
- list of items to select from
removeFlag
boolean removeFlag
- if selection went ok
cancelButton
java.awt.Button cancelButton
- cancel w/o removing
removeButton
java.awt.Button removeButton
- remove
doneButton
java.awt.Button doneButton
- Done button
this$0
PopupOrderedCondChooser this$0
f
java.awt.Frame f
- Frame where dialog box is added
msg
java.lang.String msg
- Message for dialog box
yesMsg
java.lang.String yesMsg
- Yes label for dialog box
noMsg
java.lang.String noMsg
- No label for dialog box
okFlag
boolean okFlag
- flag from OK button
this$0
PopupOrderedCondChooser this$0
pcc
PopupOrderedCondChooser pcc
- parent class
oclLd
PopupOrderedCondChooser.OclListData oclLd
- instance of OclListData
bl
java.awt.BorderLayout bl
- main layout
labelGL
java.awt.GridLayout labelGL
- labels GridLayout to create condition form
tfGL
java.awt.GridLayout tfGL
- TextFields GridLayout to create condition form
labelPanel
java.awt.Panel labelPanel
- labels go here
tfPanel
java.awt.Panel tfPanel
- TextFields go here
mainPanel
java.awt.Panel mainPanel
- place both labelPanel & tfPanel to create form
nameTF
java.awt.TextField[] nameTF
- parameter names fields
valueChangedFlag
boolean valueChangedFlag
- a value was changed for THIS condition in one or more parametes, so
data will need to be saved.
nParams
int nParams
this$0
PopupOrderedCondChooser this$0
pcc
PopupOrderedCondChooser pcc
- instance of PopupOrderedCondChooser
newNameTF
java.awt.TextField newNameTF
- textfield for typing in new name
cancelButton
java.awt.Button cancelButton
- cancel button
doneButton
java.awt.Button doneButton
- done button
stringValidFlag
boolean stringValidFlag
- This is set if the name the user types is valid
newString
java.lang.String newString
- used to return the string the user types in
cc
PopupOrderedCondChooser cc
- instance of PopupOrderedCondChooser
id
int id
- id # for this instance
maxConditions
int maxConditions
- the MAX # of conditions specified by MAExplorer
addChangePosFlag
boolean addChangePosFlag
- if can move SELECTED entry up/down
remoteFlag
boolean remoteFlag
- true if using other prj data/ta
isWinPCflag
boolean isWinPCflag
- The system is a windows PC
valueChangedFlag
boolean valueChangedFlag
- value changed
remainderMeh
PopupOrderedCondChooserGUI.MouseEventHandler remainderMeh
- handle mouse events for text areas for remTextArea LEFT
selectMeh
PopupOrderedCondChooserGUI.MouseEventHandler selectMeh
- handle mouse events for text areas for selTextArea RIGHT
remTextArea
java.awt.TextArea remTextArea
- REMAINDER objs
selTextArea
java.awt.TextArea selTextArea
- SELECTED obj list
addButton
java.awt.Button addButton
- Move the Remainder entry to Selected
delButton
java.awt.Button delButton
- Nove the Selected entry to Remainder
addAllButton
java.awt.Button addAllButton
- Move ALL Remainder entries to Selected
rmvAllButton
java.awt.Button rmvAllButton
- Move ALL Selected entries to Remainder
upButton
java.awt.Button upButton
- Move SELECTED entry up if possible
downButton
java.awt.Button downButton
- Move SELECTED entry down if possible
controlPanel
java.awt.Panel controlPanel
- control panel for main ok/reset buttons
buttonPanel
java.awt.Panel buttonPanel
- buttons panel
prjListPanel
java.awt.Panel prjListPanel
- project prj ta
objButtonPanel
java.awt.Panel objButtonPanel
- set prj button
objListTApanel
java.awt.Panel objListTApanel
- obj list remTextArea
upDownPanel
java.awt.Panel upDownPanel
- panel with up/down buttons
addDelAllButtonPanel
java.awt.Panel addDelAllButtonPanel
- add,del,all buttons
selectedPanel
java.awt.Panel selectedPanel
- SELECTED list
changePosPanel
java.awt.Panel changePosPanel
- change up/down position panel
remTextAreaLabel
java.awt.Label remTextAreaLabel
- label under remTextArea
selTextAreaLabel
java.awt.Label selTextAreaLabel
- label under selTextArea
useAbove
java.awt.Label useAbove
- optional label if not to use remTextArea from above
lTitle
java.awt.Label lTitle
- label for title for entire GUI window
taRows
int taRows
- rows/text area
taCols
int taCols
- columns/text area
origRemObjsSize
int origRemObjsSize
- REMAINDER list size
origSelObjsSize
int origSelObjsSize
- SELECTED list size
remObjListSize
int remObjListSize
- REMAINDER list size
selObjListSize
int selObjListSize
- SELECTED list size
title
java.lang.String title
- title for entire GUI window
remLabelName
java.lang.String remLabelName
- label for SELECTED LEFT text area
selLabelName
java.lang.String selLabelName
- label for REMAINDER RIGHT text area
origRemObjs
java.lang.String[] origRemObjs
- original REMAINDER list
origSelObjs
java.lang.String[] origSelObjs
- original SELECTED list
remObjList
java.lang.String[] remObjList
- REMAINDER list of cond objects, returned if needed
selObjList
java.lang.String[] selObjList
- SELECTED list of cond object names to be returned
ccGUI
PopupOrderedCondChooserGUI ccGUI
- This is either the remote instance or 'this' instance of PopupOrderedCondChooserGUI
for the instance of REMAINDER to use.
titleFont
java.awt.Font titleFont
- font used by title
labelFont
java.awt.Font labelFont
- font used by label
dataFont
java.awt.Font dataFont
- font used by data
buttonFont
java.awt.Font buttonFont
- button font
ccGUIpanel
java.awt.Panel ccGUIpanel
- main GUI panel
parentWindow
java.lang.Object parentWindow
- parent window
taRows
int taRows
- working row size of text area
taCols
int taCols
- working column size of text area
prjTbl
Table prjTbl
- "Project-Name Project-Dir" table
nRows
int nRows
- # of non-null Table rows
idxPrjName
int idxPrjName
- Table field: "Project-Name"
idxPrjDir
int idxPrjDir
- Table field: "Project-Directory"
mae
MAExplorer mae
frame
java.awt.Frame frame
checkBoxesSP
java.awt.ScrollPane checkBoxesSP
checkBoxPanel
java.awt.Panel checkBoxPanel
- to put checkBoxPanel in so can scroll
controlPanel
java.awt.Panel controlPanel
- to put checkBoxPanel in so can scroll
nameListCB
java.awt.Checkbox[] nameListCB
- holds "Done" and "Cancel" buttons
nameList
java.lang.String[] nameList
- [0:nList-1] checkboxes
valueList
boolean[] valueList
- [0:nList-1] values
doneButton
java.awt.Button doneButton
- [0:nList-1] values
cancelButton
java.awt.Button cancelButton
- [0:nList-1] values
titleLbl
java.awt.Label titleLbl
nList
int nList
- holds title at top
title
java.lang.String title
- # of elements in the list
|
Class Rtest implements Serializable |
mja
MaeJavaAPI mja
mjaProperty
MJAproperty mjaProperty
mjaReport
MJAreport mjaReport
mjaUtil
MJAutil mjaUtil
mjaReval
MJAReval mjaReval
- instance of Reval
mr
MJAReval mr
DBUG_FLAG
boolean DBUG_FLAG
rt
Rtest rt
mjaReval
MJAReval mjaReval
- instance of Reval
mr
MJAReval mr
rgd
RgenDemo rgd
- R demo code generator
nAnalyses
int nAnalyses
- The total number of analyses in the RLO database
nDemoAnalyses
int nDemoAnalyses
- The number of "Demo" analyses in the RLO database.
Demo analyses use the generated .R script options specified
by genRbits.
clientName
java.lang.String clientName
- Name of the client
clientPrefixName
java.lang.String clientPrefixName
- Prefix Name of the client
clientPrjPath
java.lang.String clientPrjPath
- Client current project path. This path will hold
the Temp/ and Report/ directories.
E.g., "../MAE" startup for MAExplorer client
clientBrowserTitle
java.lang.String clientBrowserTitle
- Client current browser title for this database
clientDatabase
java.lang.String clientDatabase
- Client current database
javaHome
java.lang.String javaHome
osName
java.lang.String osName
fileSep
java.lang.String fileSep
userDir
java.lang.String userDir
isWindowsFlag
boolean isWindowsFlag
- Flag set if running on a Windows computer
dbugFlag
boolean dbugFlag
- Flag set debugging - toggled by dbugbox if DBUG_FLAG is set
guiReadyFlag
boolean guiReadyFlag
- set if GUI is ready for action!
showDemoRLOsFlag
boolean showDemoRLOsFlag
- Flag show Demo RLOs in menu - toggled by showDemoRLOsCheckbox
appendTextFlag
boolean appendTextFlag
- Flag for append text and resetting cursor to end of TextArea
preferredHeight
int preferredHeight
- preferred height size of frame
preferredWidth
int preferredWidth
- preferred width size of frame
nRows
int nRows
- # of rows size of text area for reporting
nCols
int nCols
- # of columns size of text area for reporting
spaces
java.lang.String spaces
- Spaces
saveReportAsTextFileFlag
boolean saveReportAsTextFileFlag
- Flag enabled if doing "SaveAs"
titleFont
java.awt.Font titleFont
- fonts for labeling full image title etc.
msgFont
java.awt.Font msgFont
- fonts for labeling subtitle for each panel in image
topPanel
java.awt.Panel topPanel
- top panel holding the buttonPanel and the msgTA TextField
inputPanel
java.awt.Panel inputPanel
- input panel to hold scriptChoice
buttonPanel
java.awt.Panel buttonPanel
- button control panel
saveAllDemoRLOsButton
java.awt.Button saveAllDemoRLOsButton
- Save All Demo RLOs button if "Show Demo RLOs" is set. This generates
all RLO/DemoRscript*.rlo and R/DemoRscript*.R files for later
use by Client next time it starts up.
evalButton
java.awt.Button evalButton
- "Evaluate" window button
showPlotsButton
java.awt.Button showPlotsButton
- "Show generated plot(s)" window button
showRscriptButton
java.awt.Button showRscriptButton
- "Show R script" current R script button
clearReportButton
java.awt.Button clearReportButton
- "Clear report" to clear the text area
saveasButton
java.awt.Button saveasButton
- "SaveAs" window button
closeButton
java.awt.Button closeButton
- "Close" window button
newRLOButton
java.awt.Button newRLOButton
- "New RLO" to create new RLO
editRLOButton
java.awt.Button editRLOButton
- "Edit RLO" to edit existing RLO
showRLOButton
java.awt.Button showRLOButton
- "Show RLO" window button
deleteRLOButton
java.awt.Button deleteRLOButton
- "Delete RLO" window button
helpButton
java.awt.Button helpButton
- "Help Msg" window button
showDemoRLOsCheckbox
java.awt.Checkbox showDemoRLOsCheckbox
- Show Demo RLOs checkbox toggles showDemoRLOsFlag. This controls the
entries in the scriptChoice list.
dbugCheckbox
java.awt.Checkbox dbugCheckbox
- dbug checkbox toggles output being appended to reportText window
msgTF
java.awt.TextField msgTF
- Text message report line
msgColor
java.awt.Color msgColor
- Text message foreground color that may be changed
msgBkgrd
java.awt.Color msgBkgrd
- Text message background color that may be changed
dataTF
java.awt.TextField dataTF
- Text data report line
dataColor
java.awt.Color dataColor
- Text data report foreground color that may be changed
dataBkgrd
java.awt.Color dataBkgrd
- Text data report background color that may be changed
inputTF
java.awt.TextField inputTF
- Text input data line
reportTextArea
java.awt.TextArea reportTextArea
- Text area to draw reportText that is returned from performing the eval
of the .R script
reportText
java.lang.String reportText
- text for TextArea
helpMsg
java.lang.String helpMsg
- Help text
scriptChoice
java.awt.Choice scriptChoice
- Choice to select an R script to use from analysis[0:nAnalyses-1].
The current script is in curAnalysis
pe
PopupEditRscript pe
mae
MAExplorer mae
- link to global instance of MAExplorer
map
Maps map
- link to global instance of Maps
cdb
CompositeDatabase cdb
- link to global instance of CompositeDatabase
cfg
Config cfg
- link to global instance of Config
fc
Filter fc
- link to global instance of Filter
msR
MaHybridSample msR
- link to current sample
gct
GeneClass gct
- link to global instance of GeneClass
is
ArrayScroller is
- Parent class
isName
java.lang.String isName
- name of ArrayScroller parent
xyCQ
java.awt.Point[] xyCQ
- link to ms.xyCQ[] coordinates of spots
markerShape
int markerShape
- either MARKER_PLUS or MARKER_CIRCLE
addPixels
int addPixels
- extra pixels for circles
xBase
int xBase
- + base address of ULHC of clipped image in
image canvas used in last paint
yBase
int yBase
- + base address of ULHC of clipped image in
image canvas used in last paint
xImg
int xImg
yImg
int yImg
xObj
int xObj
- eventHndlr set (x,y) object position
yObj
int yObj
- eventHndlr set (x,y) object position
xRelMap
int xRelMap
yRelMap
int yRelMap
preferredHeight
int preferredHeight
preferredWidth
int preferredWidth
iWidth
int iWidth
- size of array area within canvas
iHeight
int iHeight
- size of array area within canvas
extraWidth
int extraWidth
- status area MaHPquantTable.X_SPOTQ_OFFSET
extraHeight
int extraHeight
- status area MaHPquantTable.Y_SPOTQ_OFFSET
scWidth
int scWidth
- pImage: iWidth+extraWidth of the actual canvas
scHeight
int scHeight
- pImage: iHeight+extraHeight of the actual canvas
showedHPmouseOverFlag
boolean showedHPmouseOverFlag
- displayed HP MouseOver
showedGeneMouseOverFlag
boolean showedGeneMouseOverFlag
- displayed Gene MouseOver
ctrlMod
boolean ctrlMod
- CTRL/Mouse
shiftMod
boolean shiftMod
- SHIFT/Mouse
drawIntoImageFlag
boolean drawIntoImageFlag
- set if draw clustergram to GIF file
oGifFileName
java.lang.String oGifFileName
- GIF output file if used
objColor
java.awt.Color objColor
- object color
targetColor
java.awt.Color targetColor
- cross-hairs color
smallFont
java.awt.Font smallFont
- small char font - 12pt
mediumFont
java.awt.Font mediumFont
- small char font - 12pt
xyObj
java.awt.Point xyObj
- current point (xObj,yObj) on event
fromPoint
java.awt.Point fromPoint
- mousePressed record
toPoint
java.awt.Point toPoint
- mouseDragged record
mae
MAExplorer mae
popupName
java.lang.String popupName
- link to global instance
popupPropertyBits
int popupPropertyBits
- ARG: for PopupRegistry
title
java.lang.String title
- ARG: for PopupRegistry
epov
ExprProfileOverlay epov
- Overlay EP plots
epsp
ExprProfileScrollPane epsp
- scrollable panel of ExprProfilePanel's
epPane
java.awt.ScrollPane epPane
- Scrollable panel
gp
java.awt.Panel gp
- Grid panel
mlToUse
GeneList mlToUse
- Master GeneList being used
nGenes
int nGenes
- # of genes in expression profile
frameWidth
int frameWidth
- this frame size computed
frameHeight
int frameHeight
- this frame size computed
epspStatusLabel
java.awt.Label epspStatusLabel
mouseOverCheckBox
java.awt.Checkbox mouseOverCheckBox
showErrBarsCheckBox
java.awt.Checkbox showErrBarsCheckBox
closeButton
java.awt.Button closeButton
plotStyleButton
java.awt.Button plotStyleButton
zoomBarsButton
java.awt.Button zoomBarsButton
showEGLButton
java.awt.Button showEGLButton
showFilteredLinesButton
java.awt.Button showFilteredLinesButton
saveAsButton
java.awt.Button saveAsButton
showErrBarsFlag
boolean showErrBarsFlag
- Flag allowing the plotting of error bars
hasMeanPlotsFlag
boolean hasMeanPlotsFlag
- Flag indicating that mean values should be plotted
plotStyleMode
int plotStyleMode
- Mode for plotting points in the expr profile
where: 0=(bar) line, 1=circle, 2=curve
zoomBarsMag
int zoomBarsMag
- data magnification 1X, 2X, 5X, 10X, 20X
hpDataNbrA
int[] hpDataNbrA
- opt. # data @ each gene avg
hpDataMnA
float[][] hpDataMnA
- opt. Mean data @ each HP sample
hpDataSDA
float[][] hpDataSDA
- opt.S.D. @ each HP sample
nMnGenes
int nMnGenes
- # of mean nodes
showEGLlinesFlag
boolean showEGLlinesFlag
showFilteredLinesFlag
boolean showFilteredLinesFlag
mae
MAExplorer mae
- link to global MAExplorer instance
title
java.lang.String title
- ARG: title of popup plot
plotMode
int plotMode
- Plot mode: one of the mae.PLOT_xxxx values
frameWidth
int frameWidth
- working frame size width
frameHeight
int frameHeight
- working frame size neight
popupName
java.lang.String popupName
- ARG: popup name for PopupRegistry
popupPropertyBits
int popupPropertyBits
- ARG: property bius for PopupRegistry
buttonFont
java.awt.Font buttonFont
- cell label font
sPanel
java.awt.Panel sPanel
- Panel that holds scrollable canvas
vertLBscr
java.awt.Scrollbar vertLBscr
- vertical LowerBound scrollbar for canvas
vertUBscr
java.awt.Scrollbar vertUBscr
- vertical UpperBound scrollbar for canvas
horizLBscr
java.awt.Scrollbar horizLBscr
- horizontal LowerBound scrollbar for canvas
horizUBscr
java.awt.Scrollbar horizUBscr
- horizontal UpperBound scrollbar for canvas
mouseOverCheckBox
java.awt.Checkbox mouseOverCheckBox
- Checkbox to toggle Show "Mouse-over info"
closeButton
java.awt.Button closeButton
- close window button
histBinRangeButton
java.awt.Button histBinRangeButton
- histogram (intens/ratio) bin range button
reFilterHistButton
java.awt.Button reFilterHistButton
- reFilterHist/NoreFilterHist button
scalingButton
java.awt.Button scalingButton
- [DEPRICATED] Linear/Log button
nonFilteredGenesButton
java.awt.Button nonFilteredGenesButton
- non-Filtered genes button
saveAsButton
java.awt.Button saveAsButton
- "SaveAs" GIF image button
histBinRange
java.lang.String histBinRange
- Histogram (intens/ratio) bin range button. This button will
contain values: "= ", "< ", "> ", "<>", "><"
histBinMode
int histBinMode
- Histogram Bind Mode using
TH_xx: "= " is 1, "< " is 2, "> " is 3, "<>" is 4, "><" is 5
maxStepsScr
int maxStepsScr
- number of prewired scroller steps
visibleScr
int visibleScr
- scrollbar's 'visible' amount
outsideRangeFlag
boolean outsideRangeFlag
- flag: toggle if "><" hist range
reFilterHistFlag
boolean reFilterHistFlag
- flag: toggle with reFilterHist/NoreFilterHist button
logScalingFlag
boolean logScalingFlag
- flag: toggle with Linear/Log button
showNonFilteredGenesFlag
boolean showNonFilteredGenesFlag
- flag: toggle non-Filtered genes button
defGifFile
java.lang.String defGifFile
- default output .gif file name
dwSP
DrawScatterPlot dwSP
- instance of DrawScatterPlot if drawing a scatter plot
dwH
DrawHistogram dwH
- instance of DrawHistogram if drawing a scatter plot
dwRH
DrawRatioHistogram dwRH
- instance of DrawRatioHistogram if drawing a scatter plot
dwCG
DrawClusterGram dwCG
- instance of DrawClusterGram if drawing a scatter plot
mae
MAExplorer mae
- link to global MAExplorer instance
report
Report report
- Report instance to show
tFields
java.lang.String[] tFields
- ARG: [maxCols] Table field names from user
tData
java.lang.String[][] tData
- ARG: user Table data [0:maxRows-1][0:maxCols-1]
dataURL
java.lang.String[][] dataURL
- ARG: if url [0:maxRows-1][0:maxCols-1] from
and not null, use this for URL
altFieldNames
java.lang.String[] altFieldNames
- ARG: [maxCols] if ! null - same for all cells
prepData
java.lang.String[][] prepData
- displayed data [0:prepRows-1][0:prepCols-1]
cellFormat
int[] cellFormat
- ARG: cell type [0:maxCols] fields which are urls
is Spreadsheet.CELL_NOP, .CELL_URL, or .CELL_EXPR_PROFILE
prepHdrPos
int prepHdrPos
- location of col clicked in prepData
virtualHdrPos
int virtualHdrPos
- location of col clicked in virData
clickedCellRow
int clickedCellRow
- keep track of last clicked cell
clickedCellCol
int clickedCellCol
- keep track of last clicked cell
oldTagRow
int oldTagRow
oldTagCol
int oldTagCol
- old tag col for clicked cell color (before)
tagRow
int tagRow
- tag row for current clicked cell color
tagCol
int tagCol
- tag col for current clicked cell color
prepRows
int prepRows
- # rows in prepData table
prepCols
int prepCols
- # cols in prepData table
lastRow
int lastRow
- ARG: end of table data to use, counts from 0?
startRow
int startRow
- ARG: start of table data to use, counts from 0 ?
tRows
int tRows
- ARG: # rows in Table data
tCols
int tCols
- ARG: # cols in Table data
fontSize
int fontSize
- integer value of fontSizeStr
title
java.lang.String title
- ARG: title of spreadsheet
headerName
java.lang.String headerName
- header name for col clicked on in virData
fontSizeStr
java.lang.String fontSizeStr
- ARG: font size
popupName
java.lang.String popupName
- ARG: for PopupRegistry
popupPropertyBits
int popupPropertyBits
- ARG: for PopupRegistry
rows
int rows
- rows
cols
int cols
- cols
cellUrlFont
java.awt.Font cellUrlFont
- cell URL font
cellDataFont
java.awt.Font cellDataFont
- cell data font
buttonFont
java.awt.Font buttonFont
- cell label font
frame
java.awt.Frame frame
- frame which holds popup spreadsheet
ss
SpreadSheet ss
- SpreadSheet objecyt
cb
java.awt.Checkbox cb
- Checkbox
urlViewerFlag
boolean urlViewerFlag
- button for browser control
urlPopupFlag
boolean urlPopupFlag
- popup browser flag
headerClicked
java.awt.Color headerClicked
- color for header when click on cell
cellClicked
java.awt.Color cellClicked
- clicked color for cell color in spreadsheet
cellReg
java.awt.Color cellReg
- normal color for cell color in spreadsheet
mae
MAExplorer mae
- link to global MAExplorer nstance
mbf
MenuBarFrame mbf
- link to global instance
popupName
java.lang.String popupName
- ARG: name for PopupRegistry
popupPropertyBits
int popupPropertyBits
- ARG: property bits of window for PopupRegistry
allGenesPlotButton
java.awt.Button allGenesPlotButton
- multipurpose button that toggles between:
"Go 'Cluster gene counts' " for "allGenes" (cluster counts) and
"Go 'Cluster single genes'" for "singleGene" (similar genes).
saveAsButton
java.awt.Button saveAsButton
- "SaveAs" .txt button
savedMsg
java.lang.String savedMsg
- message after Saved Txt into file
textReport
java.lang.String textReport
- copy of text in textArea
defTxtFile
java.lang.String defTxtFile
textarea
java.awt.TextArea textarea
- Text area GUI for main report
optReportMode
int optReportMode
- Optional Report mode if > 0
fntSize
int fntSize
- font size
nRows
int nRows
- # of character rows to show
nCols
int nCols
- # of character cols to show
alertOK
boolean alertOK
- Flag: set true if popupName is "ALERT"
mode
int mode
- mode of operation used in creating this
window. Used in how we close the window
mae
MAExplorer mae
- link to global MAExplorer instance
sp
SSspreadPanel sp
- link to local SSspreadPanel instance
sv
SSscrollVertical sv
- vertical spreadsheet scroller instance
sh
SSscrollHorizontal sh
- horizontal spreadsheet scroller instance
fontSize
int fontSize
- font size number for cell entries
prepRows
int prepRows
- original # prep rows for prepDataOrig[0:prepRows-1][0:prepCols-1]
sizes w/ 2 extra col & 2 extra rows.
Col 0 and Row 0 are NULLs.
Col 1 rows [1:prepRows] is 1.2.3.4.5. prepRows..
Row 1 cols [1:prepCols] is F1, F2, F3,...
prepCols
int prepCols
- original # prep columns for prepDataOrig[0:prepRows-1][0:prepCols-1]
sizes w/ 2 extra col & 2 extra rows.
Col 0 and Row 0 are NULLs.
Col 1 rows [1:prepRows] is 1.2.3.4.5. prepRows..
Row 1 cols [1:prepCols] is F1, F2, F3,...
virRows
int virRows
- virtual row size of prepDataEdit[0:rows-1][0:cols-1]
This also inclues the field names in the top row
and the row # in the left column
virCols
int virCols
- virtual column sizes of prepDataEdit[0:rows-1][0:cols-1]
This also inclues the field names in the top row
and the row # in the left column
prepDataOrig
java.lang.String[][] prepDataOrig
- ARG:orig. prepDataOrig[0:prepRows-1][0:prepCols-1]
dataURL
java.lang.String[][] dataURL
- ARG: opt. URL to use if not null
then sizeof [prepRows][prepCols](??? CHECK???)
title
java.lang.String title
- ARG: user title
cellUrlFont
java.awt.Font cellUrlFont
- ARG: cell URL font
cellDataFont
java.awt.Font cellDataFont
- ARG: cell data font
buttonFont
java.awt.Font buttonFont
- ARG: cell label font
cellFormat
int[] cellFormat
- ARG: cell type [cols] fields is CELL_xxxx
urlPopupFlag
boolean urlPopupFlag
- popup browser flag
ssp
ShowSpreadsheetPopup ssp
- link to global instance of SpreadsheetPopup
titlePanel
java.awt.Panel titlePanel
- title panel for of spreadsheet
spreadPanel
SSspreadPanel spreadPanel
upperHorzBounds
int upperHorzBounds
- upper bounds on scroller
oldHorzValue
int oldHorzValue
- upper bounds on scroller
currentHorzValue
int currentHorzValue
- upper bounds on scroller
spreadPanel
SSspreadPanel spreadPanel
upperVertBounds
int upperVertBounds
- upper bounds on scroller
oldVertValue
int oldVertValue
- keep track of oldvalue
curVertValue
int curVertValue
- keep track of oldvalue
mae
MAExplorer mae
cells
SStextArray cells
- the array of SStextCell cells
currentValueV
int currentValueV
currentValueH
int currentValueH
positionX
int positionX
- ULHC base address starting at (1,1)
positionY
int positionY
- ULHC base address starting at (1,1)
sv
SSscrollVertical sv
- scroll bars
sh
SSscrollHorizontal sh
status
SSstatusBar status
- [RC] & full cell contents displayed @top
dataFontSize
java.awt.Font dataFontSize
- Calculated default or overidden
headerFontSize
java.awt.Font headerFontSize
- Calculated default or overidden
headerClickedCol
int headerClickedCol
index
int[] index
- for sorting
virRows
int virRows
- ARG: "virtual screen" size that is visible
virCols
int virCols
- ARG: "virtual screen" size
prepRows
int prepRows
- ARG: user data size
prepCols
int prepCols
- ARG: user data size
fontSize
int fontSize
- ARG: only if no fonts specified
dataURL
java.lang.String[][] dataURL
- opt. data for URLs if not null [0:prepRows-1][0:prepCols-1]
prepDataEdit
java.lang.String[][] prepDataEdit
- "virt. screen" [1:prepRows-1][1:prepCols-1]
prepDataOrig
java.lang.String[][] prepDataOrig
- ARG orig. data[1:prepRows-1][1:prepCols-1]
cellUrlFont
java.awt.Font cellUrlFont
- ARG: cell URL font
cellDataFont
java.awt.Font cellDataFont
- ARG: cell data font
buttonFont
java.awt.Font buttonFont
- ARG: cell label font
locRow
int locRow
locCol
int locCol
oldPosition
int oldPosition
- keep track of col last clicked
offSet
int offSet
cellFormat
int[] cellFormat
- ARG: cell type fields[0:cols-1] one of CELL_NOP,CELL_URL,
CELL_EXPR_PROFILE in user data space...
ssp
ShowSpreadsheetPopup ssp
- pass down globals
urlPopupFlag
boolean urlPopupFlag
- popup browser flag
sortAsendDesendFlag
boolean sortAsendDesendFlag
- keep track of desend/ascending
lay
java.awt.GridLayout lay
EXCELMAXLABEL
int EXCELMAXLABEL
mae
MAExplorer mae
- max number col with alphabet
coordsNumber
java.awt.Label coordsNumber
content
SStextCell content
previousOldContent
java.lang.String previousOldContent
oldContent
java.lang.String oldContent
prepDataEdit
java.lang.String[][] prepDataEdit
virRows
int virRows
virCols
int virCols
positionX
int positionX
positionY
int positionY
urlPopupFlag
boolean urlPopupFlag
ssp
ShowSpreadsheetPopup ssp
- popup browser flag
cell
SStextCell cell
txt
SStextCell txt
txtOld
SStextCell txtOld
dataRow
int dataRow
- virtual coordinate for status bar
dataCol
int dataCol
- virtual coordinate for status bar
i
int i
- grid index
j
int j
- grid index
nextRow
SStextCell nextRow
nextCol
SStextCell nextCol
mae
MAExplorer mae
- link to global MAExplorer instance
cfg
Config cfg
- link to global Config instance
util
Util util
- link to global Util instance
DEFAULT_PANEL_WIDTH
int DEFAULT_PANEL_WIDTH
- default width size of state scroller panel
DEFAULT_PANEL_HEIGHT
int DEFAULT_PANEL_HEIGHT
- default height size of state scroller panel
PREFERRED_PANEL_HEIGHT
int PREFERRED_PANEL_HEIGHT
- max width size of state scroller panel
PREFERRED_PANEL_WIDTH
int PREFERRED_PANEL_WIDTH
- max height size of state scroller panel
GRIDCOL
int GRIDCOL
- size of grid for panel
scrPos
java.awt.Point scrPos
- Normal position for showing selected state. If showing
all states, then move Vert position to near top
allowPopdownOnWindowClosing
boolean allowPopdownOnWindowClosing
- Flag: allow popdown if orig. window closing
doRepaint
boolean doRepaint
runImageOptimizer
boolean runImageOptimizer
runClusterAnalysis
boolean runClusterAnalysis
runKmeansClusterAnalysis
boolean runKmeansClusterAnalysis
runFilter
boolean runFilter
sbSize
int[] sbSize
- size of scale in Scroller space
sbUpperBound
float[] sbUpperBound
- Note: upper bounds in STATE space
sbLowerBound
float[] sbLowerBound
- Note: lower bounds in STATE space
sbCurValue
float[] sbCurValue
- current & initial (STATE) values of scrollbar
sbLTidx
int[] sbLTidx
- corresponding LT scroller integer bounds
sbGTidx
int[] sbGTidx
- corresponding GT scroller integer bounds
sbPrecision
int[] sbPrecision
- # of digits in scroller value labels
sbNonLinearScale
boolean[] sbNonLinearScale
- Flags for using a nonlinear vernier in the SCROLLER CONTROLs
useFilterCounters
int[] useFilterCounters
- # of filters dependent on each slider. Each filter
that requires that slider will increment the counter
when it is enabled and decrement the counter when
it is disabled.
title
java.lang.String title
- holds title string for state scroller GUI
lowerControlPanel
java.awt.Panel lowerControlPanel
- holds buttons, textAreas, etc for state scroller GUI
doneButton
java.awt.Button doneButton
- pop down (hide) the box - only in adjust all scrollers mode.
Normally, can only pop it down if there are NO associated data Filters.
applyButton
java.awt.Button applyButton
- Apply the parameters to the data filters. Only in adjust all scrollers
mode. Normally, automatically apply it by calling the data filters if not
adjusting all scrollers mode.
adjustAllButton
java.awt.Button adjustAllButton
- pop down current mode and popup adjust all sliders
mouseoverTA
java.awt.TextArea mouseoverTA
- mouseover TextArea
titleLabel
java.awt.Label titleLabel
- Label for title
sbLblName
java.awt.Label[] sbLblName
- label of Name to left of scrollbar
sbLblValue
java.awt.Label[] sbLblValue
- label of Values to right of scrollbar
sbBar
java.awt.Scrollbar[] sbBar
- list of scroll bars
sbActive
boolean[] sbActive
- Flags: true if scroll bars are active
pgrid
java.awt.Panel pgrid
- holds the Scrollbar (SB) panels
bgColor
java.awt.Color bgColor
- optional background color ...
newFontLbl
java.awt.Font newFontLbl
- font type for labels
useAllScrollersFlag
boolean useAllScrollersFlag
- Flag: force all scrollers to appear even if not used...
isVisible
boolean isVisible
- Flag: if StateScroller GUI is visible
pnlWidth
int pnlWidth
- panel size Width
pnlHeight
int pnlHeight
- panel size height
gridCol
int gridCol
- size of grid for panel
gridRow
int gridRow
- size of grid for panel
dcg
DrawClusterGram dcg
preferredHeight
int preferredHeight
preferredWidth
int preferredWidth