Serialized Form
Package edu.cmu.cs.sb.chromviewer |
DEBUG
boolean DEBUG
theFrame
javax.swing.JFrame theFrame
theDataSet
DataSetCore theDataSet
tgr
GoAnnotations.GoResults tgr
saveButton
javax.swing.JButton saveButton
copyButton
javax.swing.JButton copyButton
tabledata
java.lang.String[][] tabledata
columnNames
java.lang.String[] columnNames
sorter
TableSorterRoman sorter
htinames
java.util.HashSet<E> htinames
szTitle
java.lang.String szTitle
cf
ChromFrame cf
frame_width
int frame_width
frame_height
int frame_height
scale
double scale
inited
boolean inited
genomeParser
GenomeFileParser genomeParser
chromRectangles
ChromRectangle[] chromRectangles
chromNames
edu.umd.cs.piccolo.nodes.PText[] chromNames
midLine
edu.umd.cs.piccolo.nodes.PPath midLine
pc
edu.umd.cs.piccolo.PCanvas pc
buttonColor
java.awt.Color buttonColor
geneColor
java.awt.Color geneColor
colorButton
javax.swing.JButton colorButton
hsrejected
java.util.HashSet<E> hsrejected
hmaccepted
java.util.HashMap<K,V> hmaccepted
hmcolor
java.util.HashMap<K,V> hmcolor
szGeneHeader
java.lang.String szGeneHeader
chroms
Gene[] chroms
bsortsize
boolean bsortsize
sortMapping
int[] sortMapping
buttonsort
javax.swing.JButton buttonsort
DEBUG
boolean DEBUG
cf
ChromFrame cf
columnNames
java.lang.String[] columnNames
tabledata
java.lang.String[][] tabledata
saveButton
javax.swing.JButton saveButton
copyButton
javax.swing.JButton copyButton
savenamesButton
javax.swing.JButton savenamesButton
copynamesButton
javax.swing.JButton copynamesButton
alprofiles
java.util.ArrayList<E> alprofiles
sorter
TableSorter sorter
bprofileonly
boolean bprofileonly
bquery
boolean bquery
szTitle
java.lang.String szTitle
theFrame
javax.swing.JFrame theFrame
DEBUG
boolean DEBUG
cf
ChromFrame cf
columnNames
java.lang.String[] columnNames
tabledata
java.lang.String[][] tabledata
saveButton
javax.swing.JButton saveButton
copyButton
javax.swing.JButton copyButton
savenamesButton
javax.swing.JButton savenamesButton
copynamesButton
javax.swing.JButton copynamesButton
alprofiles
java.util.ArrayList<E> alprofiles
sorter
TableSorter sorter
bprofileonly
boolean bprofileonly
bquery
boolean bquery
szTitle
java.lang.String szTitle
theFrame
javax.swing.JFrame theFrame
mChangeLayout
boolean mChangeLayout
gp
GenomeFileParser gp
yp
GenomeFileParser yp
mHorizontalOrientation
boolean mHorizontalOrientation
mGeneInfo
Gene mGeneInfo
mGeneAlias
java.lang.String mGeneAlias
mWidthScale
double mWidthScale
mLeftToRight
boolean mLeftToRight
mInputListener
GeneRectangle.GeneMouseOverHandler mInputListener
nromancol
int nromancol
Package edu.cmu.cs.sb.core |
szfile
java.lang.String szfile
list
javax.swing.JList list
data
java.util.Vector<E> data
mainButton
javax.swing.JButton mainButton
removeButton
javax.swing.JButton removeButton
okButton
javax.swing.JButton okButton
viewButton
javax.swing.JButton viewButton
allButton
javax.swing.JRadioButton allButton
indivButton
javax.swing.JRadioButton indivButton
defaultColor
java.awt.Color defaultColor
fc
javax.swing.JFileChooser fc
frame
javax.swing.JFrame frame
names
java.util.Vector<E> names
bColor
java.awt.Color bColor
typeHButton
javax.swing.JButton typeHButton
theTableSorter
TableSorter theTableSorter
columnNames
java.lang.String[] columnNames
- An array of the column header names
data
java.lang.Object[][] data
- A multi-dimensional array of data values
tga
GoAnnotations tga
- The GoAnnotations object to update based on which genes are selected
columnNames
java.lang.String[] columnNames
- An array of the column header names
data
java.lang.Object[][] data
- A multi-dimensional array of data values
serialVersionUID: 107L
tableModel
javax.swing.table.TableModel tableModel
viewToModel
edu.cmu.cs.sb.core.TableSorter.Row[] viewToModel
modelToView
int[] modelToView
tableHeader
javax.swing.table.JTableHeader tableHeader
mouseListener
java.awt.event.MouseListener mouseListener
tableModelListener
javax.swing.event.TableModelListener tableModelListener
columnComparators
java.util.Map<K,V> columnComparators
sortingColumns
java.util.List<E> sortingColumns
Package edu.cmu.cs.sb.drem |
szorganismsourceval
java.lang.String szorganismsourceval
szxrefsourceval
java.lang.String szxrefsourceval
btraintest
boolean btraintest
bdownloading
boolean[] bdownloading
lockpd
java.lang.Object lockpd
lockxref
java.lang.Object lockxref
npercentdone
int[] npercentdone
bexception
boolean[] bexception
nexceptions
int nexceptions
s1
long s1
bfButton
javax.swing.JRadioButton bfButton
fdrButton
javax.swing.JRadioButton fdrButton
noneButton
javax.swing.JRadioButton noneButton
bfgoButton
javax.swing.JRadioButton bfgoButton
randomgoButton
javax.swing.JRadioButton randomgoButton
initopenButton
javax.swing.JRadioButton initopenButton
initsearchButton
javax.swing.JRadioButton initsearchButton
initnoButton
javax.swing.JRadioButton initnoButton
endSearchButton
javax.swing.JButton endSearchButton
currentButton
javax.swing.JButton currentButton
statusLabel
javax.swing.JLabel statusLabel
statusLabel15
javax.swing.JLabel statusLabel15
statusLabel2
javax.swing.JLabel statusLabel2
statusLabel3
javax.swing.JLabel statusLabel3
statuscountLabel
javax.swing.JLabel statuscountLabel
szorig1val
java.lang.String szorig1val
szstaticFileval
java.lang.String szstaticFileval
szxrefval
java.lang.String szxrefval
szorig2val
java.lang.String szorig2val
szgoval
java.lang.String szgoval
szgocategoryval
java.lang.String szgocategoryval
szextraval
java.lang.String szextraval
szcategoryIDval
java.lang.String szcategoryIDval
szinitfileval
java.lang.String szinitfileval
sznumchildval
java.lang.String sznumchildval
szevidenceval
java.lang.String szevidenceval
sztaxonval
java.lang.String sztaxonval
ballowmergeval
boolean ballowmergeval
bpontoval
boolean bpontoval
bcontoval
boolean bcontoval
bfontoval
boolean bfontoval
bpenalizedmodelval
boolean bpenalizedmodelval
szmaxmissingval
java.lang.String szmaxmissingval
szexpressval
java.lang.String szexpressval
szfilterthresholdval
java.lang.String szfilterthresholdval
szlbval
java.lang.String szlbval
szalphaval
java.lang.String szalphaval
szpercentileval
java.lang.String szpercentileval
sznumberprofilesval
java.lang.String sznumberprofilesval
szsamplepvalval
java.lang.String szsamplepvalval
szmingoval
java.lang.String szmingoval
szmingolevelval
java.lang.String szmingolevelval
bstaticcheckval
boolean bstaticcheckval
ninitsearchval
int ninitsearchval
brandomgoval
boolean brandomgoval
btakelog
boolean btakelog
bstaticsearchval
boolean bstaticsearchval
ndb
int ndb
nxrefcb
int nxrefcb
nstaticsourcecb
int nstaticsourcecb
szusergann
java.lang.String szusergann
szuserFileField
java.lang.String szuserFileField
szuserxref
java.lang.String szuserxref
szepsilonval
java.lang.String szepsilonval
sznodepenaltyval
java.lang.String sznodepenaltyval
szconvergenceval
java.lang.String szconvergenceval
szprunepathval
java.lang.String szprunepathval
szdelaypathval
java.lang.String szdelaypathval
szmergepathval
java.lang.String szmergepathval
szepsilonvaldiff
java.lang.String szepsilonvaldiff
szprunepathvaldiff
java.lang.String szprunepathvaldiff
szdelaypathvaldiff
java.lang.String szdelaypathvaldiff
szmergepathvaldiff
java.lang.String szmergepathvaldiff
szseedval
java.lang.String szseedval
bmaxminval
boolean bmaxminval
ntodownload
int ntodownload
balltime
boolean balltime
bspotincluded
boolean bspotincluded
badd0
boolean badd0
orig1Label
javax.swing.JLabel orig1Label
staticFileLabel
javax.swing.JLabel staticFileLabel
xrefLabel
javax.swing.JLabel xrefLabel
xrefsourceLabel
javax.swing.JLabel xrefsourceLabel
categoryIDLabel
javax.swing.JLabel categoryIDLabel
extraLabel
javax.swing.JLabel extraLabel
compare1Label
javax.swing.JLabel compare1Label
compare2Label
javax.swing.JLabel compare2Label
alphaLabel
javax.swing.JLabel alphaLabel
corrmodelLabel
javax.swing.JLabel corrmodelLabel
maxmissingLabel
javax.swing.JLabel maxmissingLabel
filterthresholdLabel
javax.swing.JLabel filterthresholdLabel
expressLabel
javax.swing.JLabel expressLabel
maxchangeLabel
javax.swing.JLabel maxchangeLabel
percentileLabel
javax.swing.JLabel percentileLabel
lbLabel
javax.swing.JLabel lbLabel
samplepvalLabel
javax.swing.JLabel samplepvalLabel
goLabel
javax.swing.JLabel goLabel
mingoLabel
javax.swing.JLabel mingoLabel
mingolevelLabel
javax.swing.JLabel mingolevelLabel
randomgoLabel
javax.swing.JLabel randomgoLabel
epsilonLabel
javax.swing.JLabel epsilonLabel
prunepathLabel
javax.swing.JLabel prunepathLabel
delaypathLabel
javax.swing.JLabel delaypathLabel
mergeLabel
javax.swing.JLabel mergeLabel
epsilonLabeldiff
javax.swing.JLabel epsilonLabeldiff
prunepathLabeldiff
javax.swing.JLabel prunepathLabeldiff
delaypathLabeldiff
javax.swing.JLabel delaypathLabeldiff
mergeLabeldiff
javax.swing.JLabel mergeLabeldiff
numchildLabel
javax.swing.JLabel numchildLabel
seedLabel
javax.swing.JLabel seedLabel
nodepenaltyLabel
javax.swing.JLabel nodepenaltyLabel
initFileLabel
javax.swing.JLabel initFileLabel
savedModelOptionsLabel
javax.swing.JLabel savedModelOptionsLabel
filterchoiceLabel
javax.swing.JLabel filterchoiceLabel
modelLabel
javax.swing.JLabel modelLabel
convergenceJLabel
javax.swing.JLabel convergenceJLabel
orgcb
javax.swing.JComboBox orgcb
xrefcb
javax.swing.JComboBox xrefcb
staticsourcecb
javax.swing.JComboBox staticsourcecb
lognormButton
javax.swing.JRadioButton lognormButton
normButton
javax.swing.JRadioButton normButton
nonormButton
javax.swing.JRadioButton nonormButton
maxminButton
javax.swing.JRadioButton maxminButton
absButton
javax.swing.JRadioButton absButton
penalizedButton
javax.swing.JRadioButton penalizedButton
traintestButton
javax.swing.JRadioButton traintestButton
normGroup
javax.swing.ButtonGroup normGroup
modelGroup
javax.swing.ButtonGroup modelGroup
anncheck
javax.swing.JCheckBox anncheck
xrefcheck
javax.swing.JCheckBox xrefcheck
obocheck
javax.swing.JCheckBox obocheck
threewaycheck
javax.swing.JCheckBox threewaycheck
allowmergecheck
javax.swing.JCheckBox allowmergecheck
staticsearchcheck
javax.swing.JCheckBox staticsearchcheck
pcheck
javax.swing.JCheckBox pcheck
fcheck
javax.swing.JCheckBox fcheck
ccheck
javax.swing.JCheckBox ccheck
spotcheck
javax.swing.JCheckBox spotcheck
staticcheck
javax.swing.JCheckBox staticcheck
executeDialognf
javax.swing.JDialog executeDialognf
orig1Field
javax.swing.JTextField orig1Field
staticFileField
javax.swing.JTextField staticFileField
goField
javax.swing.JTextField goField
extraField
javax.swing.JTextField extraField
xrefField
javax.swing.JTextField xrefField
categoryIDField
javax.swing.JTextField categoryIDField
taxonField
javax.swing.JTextField taxonField
evidenceField
javax.swing.JTextField evidenceField
initFileField
javax.swing.JTextField initFileField
orig1Button
javax.swing.JButton orig1Button
orig2Button
javax.swing.JButton orig2Button
staticFileButton
javax.swing.JButton staticFileButton
goLabelButton
javax.swing.JButton goLabelButton
xrefButton
javax.swing.JButton xrefButton
extraButton
javax.swing.JButton extraButton
categoryIDButton
javax.swing.JButton categoryIDButton
initfileButton
javax.swing.JButton initfileButton
clusterAButton
javax.swing.JButton clusterAButton
staticFileHButton
javax.swing.JButton staticFileHButton
logHButton
javax.swing.JButton logHButton
viewButton
javax.swing.JButton viewButton
viewstaticButton
javax.swing.JButton viewstaticButton
staticsourceHButton
javax.swing.JButton staticsourceHButton
repeatButton
javax.swing.JButton repeatButton
orig1HButton
javax.swing.JButton orig1HButton
orig2HButton
javax.swing.JButton orig2HButton
advancedHButton
javax.swing.JButton advancedHButton
goLabelHButton
javax.swing.JButton goLabelHButton
categoryIDHButton
javax.swing.JButton categoryIDHButton
numchildHButton
javax.swing.JButton numchildHButton
extraHButton
javax.swing.JButton extraHButton
numberProfileHButton
javax.swing.JButton numberProfileHButton
changeHButton
javax.swing.JButton changeHButton
maxmissingHButton
javax.swing.JButton maxmissingHButton
filterthresholdHButton
javax.swing.JButton filterthresholdHButton
expressHButton
javax.swing.JButton expressHButton
corrmodelHButton
javax.swing.JButton corrmodelHButton
alphamodelHButton
javax.swing.JButton alphamodelHButton
lbHButton
javax.swing.JButton lbHButton
percentileHButton
javax.swing.JButton percentileHButton
samplegeneHButton
javax.swing.JButton samplegeneHButton
samplemodelHButton
javax.swing.JButton samplemodelHButton
samplepvalHButton
javax.swing.JButton samplepvalHButton
mingoHButton
javax.swing.JButton mingoHButton
mingolevelHButton
javax.swing.JButton mingolevelHButton
methodHButton
javax.swing.JButton methodHButton
allowmergeHButton
javax.swing.JButton allowmergeHButton
xrefsourceHButton
javax.swing.JButton xrefsourceHButton
downloadlistgoHButton
javax.swing.JButton downloadlistgoHButton
xrefHButton
javax.swing.JButton xrefHButton
presetsHButton
javax.swing.JButton presetsHButton
executeHButton
javax.swing.JButton executeHButton
spotHButton
javax.swing.JButton spotHButton
infoButton
javax.swing.JButton infoButton
viewHButton
javax.swing.JButton viewHButton
viewstaticHButton
javax.swing.JButton viewstaticHButton
evidenceHButton
javax.swing.JButton evidenceHButton
ontoHButton
javax.swing.JButton ontoHButton
taxonHButton
javax.swing.JButton taxonHButton
randomgoHButton
javax.swing.JButton randomgoHButton
threewayHButton
javax.swing.JButton threewayHButton
epsilonHButton
javax.swing.JButton epsilonHButton
prunepathHButton
javax.swing.JButton prunepathHButton
delaypathHButton
javax.swing.JButton delaypathHButton
mergepathHButton
javax.swing.JButton mergepathHButton
seedHButton
javax.swing.JButton seedHButton
staticHButton
javax.swing.JButton staticHButton
initfileHButton
javax.swing.JButton initfileHButton
initsearchHButton
javax.swing.JButton initsearchHButton
staticsearchHButton
javax.swing.JButton staticsearchHButton
filterchoiceHButton
javax.swing.JButton filterchoiceHButton
nodepenaltyHButton
javax.swing.JButton nodepenaltyHButton
modelframeworkHButton
javax.swing.JButton modelframeworkHButton
convergencePanelHButton
javax.swing.JButton convergencePanelHButton
optionsButton
javax.swing.JButton optionsButton
thespinnermingo
javax.swing.JSpinner thespinnermingo
thespinnermingolevel
javax.swing.JSpinner thespinnermingolevel
thespinnermaxmissing
javax.swing.JSpinner thespinnermaxmissing
thespinnerfilterthreshold
javax.swing.JSpinner thespinnerfilterthreshold
thespinnerexpress
javax.swing.JSpinner thespinnerexpress
thespinnersamplepval
javax.swing.JSpinner thespinnersamplepval
thespinnerepsilon
javax.swing.JSpinner thespinnerepsilon
thespinnerprunepath
javax.swing.JSpinner thespinnerprunepath
thespinnerdelaypath
javax.swing.JSpinner thespinnerdelaypath
thespinnermergepath
javax.swing.JSpinner thespinnermergepath
thespinnerseed
javax.swing.JSpinner thespinnerseed
thespinnernumchild
javax.swing.JSpinner thespinnernumchild
thespinnerconvergence
javax.swing.JSpinner thespinnerconvergence
thespinnernodepenalty
javax.swing.JSpinner thespinnernodepenalty
thespinnerepsilondiff
javax.swing.JSpinner thespinnerepsilondiff
thespinnerprunepathdiff
javax.swing.JSpinner thespinnerprunepathdiff
thespinnerdelaypathdiff
javax.swing.JSpinner thespinnerdelaypathdiff
thespinnermergepathdiff
javax.swing.JSpinner thespinnermergepathdiff
thelogcheck
javax.swing.JCheckBox thelogcheck
theOptions
javax.swing.JDialog theOptions
theRepeatList
ListDialog theRepeatList
szClusterA
java.lang.String szClusterA
battachlabels
boolean battachlabels
REALHEIGHT
double REALHEIGHT
INITLEFT
double INITLEFT
binit
boolean binit
theTimeiohmm
DREM_Timeiohmm theTimeiohmm
data
double[][] data
pmavalues
int[][] pmavalues
genenames
java.lang.String[] genenames
canvas
edu.umd.cs.piccolo.PCanvas canvas
plArray
edu.umd.cs.piccolox.nodes.PLine[] plArray
theLayer
edu.umd.cs.piccolo.PLayer theLayer
hideList
java.util.ArrayList<E> hideList
hidesigList
java.util.ArrayList<E> hidesigList
hidegolabelsList
java.util.ArrayList<E> hidegolabelsList
hidetfsetlabelsList
java.util.ArrayList<E> hidetfsetlabelsList
hidepredictlabelsList
java.util.ArrayList<E> hidepredictlabelsList
hidegenesetlabelsList
java.util.ArrayList<E> hidegenesetlabelsList
circleSet
java.util.TreeSet<E> circleSet
htColors
java.util.Hashtable<K,V> htColors
htHidden
java.util.Hashtable<K,V> htHidden
htRequired
java.util.HashSet<E> htRequired
htNodes
java.util.Hashtable<K,V> htNodes
htPathToLineSet
java.util.Hashtable<K,V> htPathToLineSet
htTextVisible
java.util.Hashtable<K,V> htTextVisible
filterStaticFrame
javax.swing.JFrame filterStaticFrame
filterGOFrame
javax.swing.JFrame filterGOFrame
defineFrame
javax.swing.JFrame defineFrame
predictFrame
javax.swing.JFrame predictFrame
keyinputFrame
javax.swing.JFrame keyinputFrame
yscaleFrame
javax.swing.JFrame yscaleFrame
saveDREMFrame
javax.swing.JFrame saveDREMFrame
saveModelFrame
javax.swing.JFrame saveModelFrame
theSelectedRec
edu.cmu.cs.sb.drem.DREMGui.SelectedNodeRec theSelectedRec
theGOFilter
DREMGui_GOFilter theGOFilter
theYScalegui
DREMGui_InterfaceOptions theYScalegui
treecopy
edu.cmu.cs.sb.drem.DREM_Timeiohmm.Treenode treecopy
genetableButton
edu.umd.cs.piccolo.PNode genetableButton
setButton
edu.umd.cs.piccolo.PNode setButton
gotableButton
edu.umd.cs.piccolo.PNode gotableButton
staticButton
edu.umd.cs.piccolo.PNode staticButton
gofilterButton
edu.umd.cs.piccolo.PNode gofilterButton
scaleButton
edu.umd.cs.piccolo.PNode scaleButton
predictButton
edu.umd.cs.piccolo.PNode predictButton
hideButton
edu.umd.cs.piccolo.PNode hideButton
timeButton
edu.umd.cs.piccolo.PNode timeButton
siginButton
edu.umd.cs.piccolo.PNode siginButton
saveDREMButton
edu.umd.cs.piccolo.PNode saveDREMButton
saveModelButton
edu.umd.cs.piccolo.PNode saveModelButton
hideText
edu.umd.cs.piccolo.nodes.PText hideText
helpButton
edu.umd.cs.piccolo.nodes.PImage helpButton
nheight
int nheight
nwidth
int nwidth
ncolortime
int ncolortime
ncircleID
int ncircleID
dheightunits
double dheightunits
dminheightunits
double dminheightunits
dwidthunits
double dwidthunits
dnodek
double dnodek
dwidthunitsInterval
double[] dwidthunitsInterval
dwidthunitsCum
double[] dwidthunitsCum
dmax
double dmax
dmin
double dmin
dkeyinputpvalue
double dkeyinputpvalue
dsplitpercent
double dsplitpercent
SPLITCOLOR
java.awt.Color SPLITCOLOR
bapplygenesetlabels
boolean bapplygenesetlabels
bapplytfsetlabels
boolean bapplytfsetlabels
bapplygolabels
boolean bapplygolabels
bholdedge
boolean bholdedge
bfiltergo
boolean bfiltergo
bfiltergeneset
boolean bfiltergeneset
bfilterinput
boolean bfilterinput
brealXaxis
boolean brealXaxis
filterText
edu.umd.cs.piccolo.nodes.PText filterText
keyInputLabelColor
java.awt.Color keyInputLabelColor
goLabelColor
java.awt.Color goLabelColor
predictLabelColor
java.awt.Color predictLabelColor
genesetLabelColor
java.awt.Color genesetLabelColor
tfLabelColor
java.awt.Color tfLabelColor
binvalidreal
boolean binvalidreal
bGOVisible
boolean[] bGOVisible
bSetVisible
boolean[] bSetVisible
bPathVisible
boolean[] bPathVisible
bTFVisible
boolean[] bTFVisible
bglobalVisible
boolean bglobalVisible
blowestbelow
boolean blowestbelow
blowestabove
boolean blowestabove
bmiddlebelow
boolean bmiddlebelow
bmiddleabove
boolean bmiddleabove
bhighestbelow
boolean bhighestbelow
bhighestabove
boolean bhighestabove
blowbelow
boolean blowbelow
blowabove
boolean blowabove
bglobalnode
boolean bglobalnode
bshowpredict
boolean bshowpredict
bshowkeyinputs
boolean bshowkeyinputs
bshowgolabels
boolean bshowgolabels
bshowtfsetlabels
boolean bshowtfsetlabels
bshowgenesetlabels
boolean bshowgenesetlabels
nKeyInputType
int nKeyInputType
nf3
java.text.NumberFormat nf3
numcolor
int numcolor
nparentcolorindex
int nparentcolorindex
htColorIDtoLinesList
java.util.Hashtable<K,V> htColorIDtoLinesList
dscaley
double dscaley
dscalex
double dscalex
htColorIDtoColor
java.util.Hashtable<K,V> htColorIDtoColor
htLineIDtoColorID
java.util.Hashtable<K,V> htLineIDtoColorID
htColorIDtoCircleList
java.util.Hashtable<K,V> htColorIDtoCircleList
storedbestpath
int[] storedbestpath
bsavedchange
boolean bsavedchange
dinitmin
double dinitmin
dinitmax
double dinitmax
lineColorsA
java.awt.Color[] lineColorsA
edgeColorsTriples
java.awt.Color[][] edgeColorsTriples
colorButton
javax.swing.JButton colorButton
tga
GoAnnotations tga
tms
TableModelSetST tms
bcluster
boolean bcluster
theFrame
javax.swing.JFrame theFrame
unapplyButton
javax.swing.JButton unapplyButton
hideButton
javax.swing.JButton hideButton
sorter
TableSorter sorter
selectgenesButton
javax.swing.JButton selectgenesButton
theDREMGui
DREMGui theDREMGui
hsTFGeneList
java.util.HashSet<E> hsTFGeneList
hsList
java.util.HashSet<E> hsList
bsplitgolabels
boolean bsplitgolabels
theSlider
javax.swing.JSlider theSlider
theDictionary
java.util.Hashtable<K,V> theDictionary
pvalLabel
javax.swing.JLabel pvalLabel
ninitval
int ninitval
pathButton
javax.swing.JRadioButton pathButton
splitButton
javax.swing.JRadioButton splitButton
enrichmentGroup
javax.swing.ButtonGroup enrichmentGroup
dsetpval
double dsetpval
bapplyset
boolean bapplyset
rootptr
edu.cmu.cs.sb.drem.DREM_Timeiohmm.Treenode rootptr
theDREMGui
DREMGui theDREMGui
theTimeiohmm
DREM_Timeiohmm theTimeiohmm
theFrame
javax.swing.JFrame theFrame
columnNames
java.lang.String[] columnNames
tabledata
java.lang.String[][] tabledata
copyButton
javax.swing.JButton copyButton
saveButton
javax.swing.JButton saveButton
colorButton
javax.swing.JButton colorButton
sorter
TableSorter sorter
hmst
DREMGui_FilterStaticModel hmst
numrows
int numrows
ptr
edu.cmu.cs.sb.drem.DREM_Timeiohmm.Treenode ptr
npathID
int npathID
nchild
int nchild
ndepth
int ndepth
nf
java.text.NumberFormat nf
nf2
java.text.NumberFormat nf2
bsplit
boolean bsplit
broot
boolean broot
columnNames
java.lang.String[] columnNames
- An array of the column header names
data
java.lang.Object[][] data
- A multi-dimensional array of data values
bnegate
boolean bnegate
theFrame
javax.swing.JFrame theFrame
colorButton
javax.swing.JButton colorButton
intersectButton
javax.swing.JRadioButton intersectButton
unionButton
javax.swing.JRadioButton unionButton
tfVals
int[] tfVals
hmst
DREMGui_FilterStaticModel hmst
sorter
TableSorter sorter
theTimeiohmm
DREM_Timeiohmm theTimeiohmm
theDREMGui
DREMGui theDREMGui
numrows
int numrows
numcols
int numcols
unapplyButton
javax.swing.JButton unapplyButton
hideButton
javax.swing.JButton hideButton
bsplitgolabels
boolean bsplitgolabels
theSlider
javax.swing.JSlider theSlider
theDictionary
java.util.Hashtable<K,V> theDictionary
pvalLabel
javax.swing.JLabel pvalLabel
ninitval
int ninitval
pathButton
javax.swing.JRadioButton pathButton
splitButton
javax.swing.JRadioButton splitButton
enrichmentGroup
javax.swing.ButtonGroup enrichmentGroup
dsetpval
double dsetpval
tga
GoAnnotations tga
bapplyset
boolean bapplyset
boveralltfeligible
boolean boveralltfeligible
noveralltfrow
int noveralltfrow
noveralltfcol
int noveralltfcol
rootptr
edu.cmu.cs.sb.drem.DREM_Timeiohmm.Treenode rootptr
complementcheck
javax.swing.JCheckBox complementcheck
columnNames
java.lang.String[] columnNames
- An array of the column header names
data
java.lang.Object[][] data
- A multi-dimensional array of data values
theDataSet
DREM_DataSet theDataSet
ntabledatasize
int ntabledatasize
columnNames
java.lang.String[] columnNames
tabledata
java.lang.String[][] tabledata
bindingpval
int[][] bindingpval
bindingpvalIndex
int[][] bindingpvalIndex
bindingpvalTF
int[][] bindingpvalTF
bindingpvalTFIndex
int[][] bindingpvalTFIndex
davg
double[] davg
dstd
double[] dstd
tfNames
java.lang.String[] tfNames
saveButton
javax.swing.JButton saveButton
staticButton
javax.swing.JButton staticButton
copyButton
javax.swing.JButton copyButton
savenamesButton
javax.swing.JButton savenamesButton
copynamesButton
javax.swing.JButton copynamesButton
sorter
TableSorter sorter
theFrame
javax.swing.JFrame theFrame
include
boolean[] include
theTimeiohmm
DREM_Timeiohmm theTimeiohmm
ninitval
int ninitval
bsplitgolabels
boolean bsplitgolabels
ballgenes
boolean ballgenes
theSlider
javax.swing.JSlider theSlider
theDictionary
java.util.Hashtable<K,V> theDictionary
szGO
java.lang.String szGO
tfVals
double[] tfVals
hmst
DREMGui_FilterGOModel hmst
sorter
TableSorter sorter
theTimeiohmm
DREM_Timeiohmm theTimeiohmm
theDREMGui
DREMGui theDREMGui
numrows
int numrows
numcols
int numcols
unapplyButton
javax.swing.JButton unapplyButton
hideButton
javax.swing.JButton hideButton
theFrame
javax.swing.JFrame theFrame
rowSM
javax.swing.ListSelectionModel rowSM
defineframe
javax.swing.JFrame defineframe
pathButton
javax.swing.JRadioButton pathButton
splitButton
javax.swing.JRadioButton splitButton
allButton
javax.swing.JRadioButton allButton
selectButton
javax.swing.JRadioButton selectButton
enrichmentGroup
javax.swing.ButtonGroup enrichmentGroup
countGroup
javax.swing.ButtonGroup countGroup
dgopval
double dgopval
pvalLabel
javax.swing.JLabel pvalLabel
colorButton
javax.swing.JButton colorButton
theDataSet
DREM_DataSet theDataSet
tga
GoAnnotations tga
rootptr
edu.cmu.cs.sb.drem.DREM_Timeiohmm.Treenode rootptr
theDataSet
DREM_DataSet theDataSet
szGoID
java.lang.String szGoID
include
boolean[] include
goinclude
boolean[] goinclude
theTimeiohmm
DREM_Timeiohmm theTimeiohmm
columnNames
java.util.Vector<E> columnNames
tabledata
java.util.Vector<E> tabledata
staticButton
javax.swing.JButton staticButton
saveButton
javax.swing.JButton saveButton
savenamesButton
javax.swing.JButton savenamesButton
copyButton
javax.swing.JButton copyButton
copynamesButton
javax.swing.JButton copynamesButton
selectButton
javax.swing.JButton selectButton
unselectButton
javax.swing.JButton unselectButton
sorter
TableSorter sorter
szTitle
java.lang.String szTitle
theFrame
javax.swing.JFrame theFrame
theDREMGui
DREMGui theDREMGui
numgoinclude
int numgoinclude
tfNames
java.lang.String[] tfNames
bindingpval
int[][] bindingpval
bindingpvalIndex
int[][] bindingpvalIndex
bindingpvalTF
int[][] bindingpvalTF
bindingpvalTFIndex
int[][] bindingpvalTFIndex
DEBUG
boolean DEBUG
theFrame
javax.swing.JFrame theFrame
theDataSet
DREM_DataSet theDataSet
tgr
GoAnnotations.GoResults tgr
saveButton
javax.swing.JButton saveButton
copyButton
javax.swing.JButton copyButton
tabledata
java.lang.String[][] tabledata
columnNames
java.lang.String[] columnNames
include
boolean[] include
storedbestpath
int[] storedbestpath
ptr
edu.cmu.cs.sb.drem.DREM_Timeiohmm.Treenode ptr
bjustgo
boolean bjustgo
sorter
TableSorter sorter
htinames
java.util.HashSet<E> htinames
szTitle
java.lang.String szTitle
npathID
int npathID
theDREMGui
DREMGui theDREMGui
theFrame
javax.swing.JFrame theFrame
theDataSet
DREM_DataSet theDataSet
tgr
GoAnnotations.GoResults tgr
saveButton
javax.swing.JButton saveButton
copyButton
javax.swing.JButton copyButton
tabledata
java.lang.String[][] tabledata
columnNames
java.lang.String[] columnNames
dweightA
double[] dweightA
include
boolean[] include
bjustgo
boolean bjustgo
sorter
TableSorter sorter
htinames
java.util.HashSet<E> htinames
szTitle
java.lang.String szTitle
theDREMGui
DREMGui theDREMGui
theSlider
javax.swing.JSlider theSlider
theSliderX
javax.swing.JSlider theSliderX
theColorSlider
javax.swing.JSlider theColorSlider
theNodeSlider
javax.swing.JSlider theNodeSlider
theFrame
javax.swing.JFrame theFrame
hideButton
javax.swing.JButton hideButton
theDictionary
java.util.Hashtable<K,V> theDictionary
theDREMGui
DREMGui theDREMGui
pvalLabel
javax.swing.JLabel pvalLabel
pvalLabelX
javax.swing.JLabel pvalLabelX
nodeLabel
javax.swing.JLabel nodeLabel
attachBox
javax.swing.JCheckBox attachBox
group
javax.swing.ButtonGroup group
uniformButton
javax.swing.JRadioButton uniformButton
realButton
javax.swing.JRadioButton realButton
autogroup
javax.swing.ButtonGroup autogroup
holdButton
javax.swing.JRadioButton holdButton
autoButton
javax.swing.JRadioButton autoButton
theSlider
javax.swing.JSlider theSlider
theSliderPercent
javax.swing.JSlider theSliderPercent
hideButton
javax.swing.JButton hideButton
colorButton
javax.swing.JButton colorButton
theDictionary
java.util.Hashtable<K,V> theDictionary
theDictionaryPercent
java.util.Hashtable<K,V> theDictionaryPercent
theDREMGui
DREMGui theDREMGui
pvalLabel
javax.swing.JLabel pvalLabel
percentLabel
javax.swing.JLabel percentLabel
group
javax.swing.ButtonGroup group
splitButton
javax.swing.JRadioButton splitButton
edgeSplitButton
javax.swing.JRadioButton edgeSplitButton
edgeFullButton
javax.swing.JRadioButton edgeFullButton
theFrame
javax.swing.JFrame theFrame
rootptr
edu.cmu.cs.sb.drem.DREM_Timeiohmm.Treenode rootptr
intersectButton
javax.swing.JRadioButton intersectButton
unionButton
javax.swing.JRadioButton unionButton
tfVals
int[] tfVals
hmst
DREMGui_PredictModel hmst
sorter
TableSorter sorter
theTimeiohmm
DREM_Timeiohmm theTimeiohmm
theDREMGui
DREMGui theDREMGui
numrows
int numrows
numcols
int numcols
hideButton
javax.swing.JButton hideButton
conditionalBox
javax.swing.JCheckBox conditionalBox
theFrame
javax.swing.JFrame theFrame
columnNames
java.lang.String[] columnNames
- An array of the column header names
data
java.lang.Object[][] data
- A multi-dimensional array of data values
theDREMGui
DREMGui theDREMGui
validExt
java.util.HashSet<E> validExt
theTimeiohmm
DREM_Timeiohmm theTimeiohmm
treecopy
edu.cmu.cs.sb.drem.DREM_Timeiohmm.Treenode treecopy
theTimeiohmm
DREM_Timeiohmm theTimeiohmm
theDREMGui
DREMGui theDREMGui
theFrame
javax.swing.JFrame theFrame
columnNames
java.lang.String[] columnNames
tabledata
java.lang.String[][] tabledata
saveButton
javax.swing.JButton saveButton
copyButton
javax.swing.JButton copyButton
goButton
javax.swing.JButton goButton
sorter
TableSorter sorter
hmst
DREMGui_FilterStaticModel hmst
numrows
int numrows
ptr
edu.cmu.cs.sb.drem.DREM_Timeiohmm.Treenode ptr
npathID
int npathID
nf
java.text.NumberFormat nf
nchild
int nchild
theDataSet
DREM_DataSet theDataSet
columnNames
java.lang.String[] columnNames
tabledata
java.lang.String[][] tabledata
bindingpvalTF
int[][] bindingpvalTF
bindingpvalTFindex
int[][] bindingpvalTFindex
davg
double[] davg
dstd
double[] dstd
tfNames
java.lang.String[] tfNames
saveButton
javax.swing.JButton saveButton
copyButton
javax.swing.JButton copyButton
staticButton
javax.swing.JButton staticButton
sorter
TableSorter sorter
theFrame
javax.swing.JFrame theFrame
include
boolean[] include
numgenes
int numgenes
theTimeiohmm
DREM_Timeiohmm theTimeiohmm
Package edu.cmu.cs.sb.stem |
canvas
edu.umd.cs.piccolo.PCanvas canvas
- The canvas on which the signifcant profile pairs are displayed
theCompareInfo
CompareInfo theCompareInfo
- The CompareInfo that this gui display
profilenodes
edu.umd.cs.piccolo.PNode[] profilenodes
- Array of the profiles associated with the original dataset
nsort
int nsort
- specifies how to sort profile pairs
bswap
boolean bswap
- If the original and comparison data sets should be swapped from their original positions
swaplock
java.lang.Object swaplock
- Used to synchronize swapping actions
szother
java.lang.String szother
- Label for the other data set in the layout whether it is the comparison or the original
szprofileclusterCAP
java.lang.String szprofileclusterCAP
- String for labels indicating if we have profile pairs or captions
thegeneplotpanel
GenePlotPanel thegeneplotpanel
- thegeneplotpanel associated with the original data set
rowplotpanel
GenePlotPanel rowplotpanel
- Interface options corresponding to data set indexed as rows in the comparison
colplotpanel
GenePlotPanel colplotpanel
- Interface options corresponding to data set currently indexed as columns in the comparison
cf
ChromFrame cf
- The chromosome viewer object
tga
GoAnnotations tga
- The GoAnnotations object
tms
TableModelSetST tms
- The table model for this table
maingui
MAINGUI2 maingui
- The maingui that this geneset connects with
theFrame
javax.swing.JFrame theFrame
- The frame in which this panel will be added
sorter
TableSorter sorter
- Controls sorting in the table
rowSM
javax.swing.ListSelectionModel rowSM
- Controls selecting and unselecting rows
selectgenesButton
javax.swing.JButton selectgenesButton
- To select the checked genes
bkmeans
boolean bkmeans
- Whether the clustering method is the STEM profile metho or kmeans clustering
thespinnerprofiles
javax.swing.JSpinner thespinnerprofiles
- Spinner for selecting profile in comparison experiment
theDataSet
STEM_DataSet theDataSet
columnNames
java.lang.String[] columnNames
tabledata
java.lang.String[][] tabledata
saveButton
javax.swing.JButton saveButton
savenamesButton
javax.swing.JButton savenamesButton
copyButton
javax.swing.JButton copyButton
copynamesButton
javax.swing.JButton copynamesButton
theFrame
javax.swing.JFrame theFrame
sorter
TableSorter sorter
xgroup
javax.swing.ButtonGroup xgroup
ygroup
javax.swing.ButtonGroup ygroup
genescalegroup
javax.swing.ButtonGroup genescalegroup
genedisplaygroup
javax.swing.ButtonGroup genedisplaygroup
scalevisibleBox
javax.swing.JCheckBox scalevisibleBox
ymaintickBox
javax.swing.JCheckBox ymaintickBox
mainprofilelineBox
javax.swing.JCheckBox mainprofilelineBox
mainprofileIDBox
javax.swing.JCheckBox mainprofileIDBox
mainprofileDetailBox
javax.swing.JCheckBox mainprofileDetailBox
colorButton
javax.swing.JButton colorButton
uniformButton
javax.swing.JRadioButton uniformButton
realButton
javax.swing.JRadioButton realButton
automaticButton
javax.swing.JRadioButton automaticButton
fixedButton
javax.swing.JRadioButton fixedButton
geneButton
javax.swing.JRadioButton geneButton
profileButton
javax.swing.JRadioButton profileButton
globalButton
javax.swing.JRadioButton globalButton
nodisplayButton
javax.swing.JRadioButton nodisplayButton
alwaysdisplayButton
javax.swing.JRadioButton alwaysdisplayButton
onlyselectedButton
javax.swing.JRadioButton onlyselectedButton
minLabel
javax.swing.JLabel minLabel
maxLabel
javax.swing.JLabel maxLabel
tickLabel
javax.swing.JLabel tickLabel
tickmainLabel
javax.swing.JLabel tickmainLabel
helpPolicyButton
javax.swing.JButton helpPolicyButton
helpScaleButton
javax.swing.JButton helpScaleButton
helpXButton
javax.swing.JButton helpXButton
helpYWindowButton
javax.swing.JButton helpYWindowButton
thespinnerminy
javax.swing.JSpinner thespinnerminy
thespinnermaxy
javax.swing.JSpinner thespinnermaxy
thespinnertick
javax.swing.JSpinner thespinnertick
thespinnertickmain
javax.swing.JSpinner thespinnertickmain
bkmeans
boolean bkmeans
themaingui
MAINGUI2 themaingui
thegeneplotFrame
javax.swing.JFrame thegeneplotFrame
DEBUG
boolean DEBUG
cf
ChromFrame cf
theDataSet
STEM_DataSet theDataSet
nprofile
int nprofile
szAssignInfo
java.lang.String szAssignInfo
columnNames
java.lang.String[] columnNames
tabledata
java.lang.String[][] tabledata
saveButton
javax.swing.JButton saveButton
copyButton
javax.swing.JButton copyButton
savenamesButton
javax.swing.JButton savenamesButton
copynamesButton
javax.swing.JButton copynamesButton
chromButton
javax.swing.JButton chromButton
alprofiles
java.util.ArrayList<E> alprofiles
sorter
TableSorter sorter
bprofileonly
boolean bprofileonly
bquery
boolean bquery
szTitle
java.lang.String szTitle
theFrame
javax.swing.JFrame theFrame
htinames
java.util.HashSet<E> htinames
DEBUG
boolean DEBUG
cf
ChromFrame cf
theDataSet
STEM_DataSet theDataSet
nprofilecluster
int nprofilecluster
clusterprofiles
java.util.ArrayList<E> clusterprofiles
szHeaderInfo
java.lang.String szHeaderInfo
szGoID
java.lang.String szGoID
szGoCombined
java.lang.String szGoCombined
bqueryset
boolean bqueryset
columnNames
java.util.Vector<E> columnNames
tabledata
java.util.Vector<E> tabledata
saveButton
javax.swing.JButton saveButton
savenamesButton
javax.swing.JButton savenamesButton
copyButton
javax.swing.JButton copyButton
copynamesButton
javax.swing.JButton copynamesButton
chromButton
javax.swing.JButton chromButton
sorter
TableSorter sorter
htinames
java.util.HashSet<E> htinames
szTitle
java.lang.String szTitle
theFrame
javax.swing.JFrame theFrame
bjustgo
boolean bjustgo
theFrame
javax.swing.JFrame theFrame
theDataSet
STEM_DataSet theDataSet
nprofile
int nprofile
tgr
GoAnnotations.GoResults tgr
szqueryset
java.lang.String szqueryset
saveButton
javax.swing.JButton saveButton
copyButton
javax.swing.JButton copyButton
tabledata
java.lang.String[][] tabledata
columnNames
java.lang.String[] columnNames
clusterArray
java.util.ArrayList<E> clusterArray
bqueryset
boolean bqueryset
bjustgo
boolean bjustgo
sorter
TableSorter sorter
htinames
java.util.HashSet<E> htinames
szTitle
java.lang.String szTitle
cf
ChromFrame cf
DEBUG
boolean DEBUG
szqueryset
java.lang.String szqueryset
theFrame
javax.swing.JFrame theFrame
theDataSet
STEM_DataSet theDataSet
nprofile
int nprofile
tgr
GoAnnotations.GoResults tgr
saveButton
javax.swing.JButton saveButton
copyButton
javax.swing.JButton copyButton
cf
ChromFrame cf
tabledata
java.lang.String[][] tabledata
columnNames
java.lang.String[] columnNames
clusterArray
java.util.ArrayList<E> clusterArray
bqueryset
boolean bqueryset
sorter
TableSorter sorter
htinames
java.util.HashSet<E> htinames
szTitle
java.lang.String szTitle
profilelookup
int[] profilelookup
ranklookup
int[] ranklookup
cluster
int[] cluster
theProfileSortRec
edu.cmu.cs.sb.stem.MAINGUI2.ProfileSortRec[] theProfileSortRec
ngenescale
int ngenescale
ngenedisplay
int ngenedisplay
bscalevisible
boolean bscalevisible
canvas
edu.umd.cs.piccolo.PCanvas canvas
thegenecolor
java.awt.Color thegenecolor
theOptions
javax.swing.JDialog theOptions
thegeneplotframe
javax.swing.JFrame thegeneplotframe
profilesortframe
javax.swing.JFrame profilesortframe
clustersortframe
javax.swing.JFrame clustersortframe
thegeneplotpanel
GenePlotPanel thegeneplotpanel
thecomparegui
CompareGui thecomparegui
profilenodes
edu.umd.cs.piccolo.PNode[] profilenodes
bsaveprofile
boolean bsaveprofile
savedcolors
java.awt.Color[] savedcolors
openProfiles
java.util.ArrayList<E> openProfiles
binvalidreal
boolean binvalidreal
cf
ChromFrame cf
clustercolors
java.awt.Color[] clustercolors
theDataSet
STEM_DataSet theDataSet
buniformXaxis
boolean buniformXaxis
bautomaticYaxis
boolean bautomaticYaxis
bdisplayID
boolean bdisplayID
bdisplayprofileline
boolean bdisplayprofileline
bdisplaymaintick
boolean bdisplaymaintick
bdisplaydetail
boolean bdisplaydetail
dtickintervalmain
double dtickintervalmain
snmsigLevel
javax.swing.SpinnerNumberModel snmsigLevel
snmnumgenes
javax.swing.SpinnerNumberModel snmnumgenes
thespinnersigLevel
javax.swing.JSpinner thespinnersigLevel
thespinnernumgenes
javax.swing.JSpinner thespinnernumgenes
browse1Button
javax.swing.JButton browse1Button
compareButtonDialog
javax.swing.JButton compareButtonDialog
compare1Label
javax.swing.JLabel compare1Label
sigLevelLabel
javax.swing.JLabel sigLevelLabel
numgenesLabel
javax.swing.JLabel numgenesLabel
compare1Field
javax.swing.JTextField compare1Field
executecompareHButton
javax.swing.JButton executecompareHButton
compare1HButton
javax.swing.JButton compare1HButton
compare2HButton
javax.swing.JButton compare2HButton
sigLevelHButton
javax.swing.JButton sigLevelHButton
numgenesHButton
javax.swing.JButton numgenesHButton
viewHButton
javax.swing.JButton viewHButton
viewButton
javax.swing.JButton viewButton
repeatButton
javax.swing.JButton repeatButton
theCompareRepeatList
ListDialog theCompareRepeatList
DEBUG
boolean DEBUG
theDataSet
STEM_DataSet theDataSet
cf
ChromFrame cf
columnNames
java.lang.String[] columnNames
tabledata
java.lang.String[][] tabledata
chromButton
javax.swing.JButton chromButton
saveButton
javax.swing.JButton saveButton
savenamesButton
javax.swing.JButton savenamesButton
copyButton
javax.swing.JButton copyButton
copynamesButton
javax.swing.JButton copynamesButton
theFrame
javax.swing.JFrame theFrame
sorter
TableSorter sorter
sizeLock
java.lang.Object sizeLock
nnewheight
int nnewheight
nnewwidth
int nnewwidth
cf
ChromFrame cf
szprofilecluster
java.lang.String szprofilecluster
szprofileclusterCAP
java.lang.String szprofileclusterCAP
totalSize
java.awt.Dimension totalSize
g2
java.awt.Graphics2D g2
theDataSet
STEM_DataSet theDataSet
nprofile
int nprofile
ncluster
int ncluster
szAssignInfo
java.lang.String szAssignInfo
szGene
java.lang.String szGene
szSpot
java.lang.String szSpot
pgrr
GoAnnotations.ProfileGORankingRec pgrr
bshowcluster
boolean bshowcluster
inames
java.util.HashSet<E> inames
ncompareprofile
int ncompareprofile
szIntersect
java.lang.String szIntersect
bonlyorder
boolean bonlyorder
noffset
int noffset
bcheckonly
boolean bcheckonly
bgosorttable
boolean bgosorttable
ranklookup
int[] ranklookup
nmidpoint
int nmidpoint
gar
GoAnnotations.Rec gar
bautomatic
boolean bautomatic
dminfixed
double dminfixed
dmaxfixed
double dmaxfixed
dtickinterval
double dtickinterval
thegeneplotpanel
GenePlotPanel thegeneplotpanel
SCREENWIDTH
int SCREENWIDTH
SCREENHEIGHT
int SCREENHEIGHT
ncolwidth
int ncolwidth
nrowheight
int nrowheight
numcols
int numcols
numrows
int numrows
profiletablex
int profiletablex
clustertablex
int clustertablex
querytabley
int querytabley
tabley
int tabley
tablewid
int tablewid
tableheight
int tableheight
nonlyx
int nonlyx
nonlyy
int nonlyy
ngosorttabley
int ngosorttabley
nonlytablewid
int nonlytablewid
ngosorttablewid
int ngosorttablewid
ngosorttablex
int ngosorttablex
profilegox
int profilegox
clustergox
int clustergox
colorlist
java.util.ArrayList<E> colorlist
DEBUG
boolean DEBUG
theDataSet
STEM_DataSet theDataSet
nprofile
int nprofile
table
javax.swing.JTable table
scrollPane
javax.swing.JScrollPane scrollPane
tabledata
java.lang.String[][] tabledata
columnNames
java.lang.String[] columnNames
clusterArray
java.util.ArrayList<E> clusterArray
maingui
MAINGUI2 maingui
tga
GoAnnotations tga
sorter
TableSorter sorter
theFrame
javax.swing.JFrame theFrame
actualButton
javax.swing.JRadioButton actualButton
expectedButton
javax.swing.JRadioButton expectedButton
rowSM
javax.swing.ListSelectionModel rowSM
defineframe
javax.swing.JFrame defineframe
boutputdir
boolean boutputdir
szBatchInputDir
java.lang.String szBatchInputDir
szBatchOutputDir
java.lang.String szBatchOutputDir
szcurrentDefaultFile
java.lang.String szcurrentDefaultFile
executeDialognf
javax.swing.JDialog executeDialognf
szorganismsourceval
java.lang.String szorganismsourceval
szxrefsourceval
java.lang.String szxrefsourceval
szchromsourceval
java.lang.String szchromsourceval
bdownloading
boolean[] bdownloading
lockpd
java.lang.Object lockpd
npercentdone
int[] npercentdone
bexception
boolean[] bexception
nexceptions
int nexceptions
pcluster
javax.swing.JPanel pcluster
s1
long s1
bfButton
javax.swing.JRadioButton bfButton
fdrButton
javax.swing.JRadioButton fdrButton
noneButton
javax.swing.JRadioButton noneButton
bfgoButton
javax.swing.JRadioButton bfgoButton
randomgoButton
javax.swing.JRadioButton randomgoButton
maxminButton
javax.swing.JRadioButton maxminButton
absButton
javax.swing.JRadioButton absButton
szorig1val
java.lang.String szorig1val
szchromval
java.lang.String szchromval
szxrefval
java.lang.String szxrefval
szorig2val
java.lang.String szorig2val
szgoval
java.lang.String szgoval
szgocategoryval
java.lang.String szgocategoryval
szextraval
java.lang.String szextraval
szcategoryIDval
java.lang.String szcategoryIDval
szevidenceval
java.lang.String szevidenceval
sztaxonval
java.lang.String sztaxonval
bpontoval
boolean bpontoval
bcontoval
boolean bcontoval
bfontoval
boolean bfontoval
szmaxmissingval
java.lang.String szmaxmissingval
szexpressval
java.lang.String szexpressval
szfilterthresholdval
java.lang.String szfilterthresholdval
szlbval
java.lang.String szlbval
szalphaval
java.lang.String szalphaval
szpercentileval
java.lang.String szpercentileval
szmaxchangeval
java.lang.String szmaxchangeval
sznumberprofilesval
java.lang.String sznumberprofilesval
szcorrmodelval
java.lang.String szcorrmodelval
szsamplegeneval
java.lang.String szsamplegeneval
szsamplepvalval
java.lang.String szsamplepvalval
szsamplemodelval
java.lang.String szsamplemodelval
szmingoval
java.lang.String szmingoval
szmingolevelval
java.lang.String szmingolevelval
brandomgoval
boolean brandomgoval
btakelog
boolean btakelog
bmaxminval
boolean bmaxminval
ballpermuteval
boolean ballpermuteval
ndb
int ndb
nK
int nK
nreps
int nreps
nMaxProfiles
int nMaxProfiles
nMaxChangeProfiles
int nMaxChangeProfiles
nxrefcb
int nxrefcb
nchromcb
int nchromcb
nclusteringmethodcb
int nclusteringmethodcb
noldcluteringmethodcb
int noldcluteringmethodcb
szusergann
java.lang.String szusergann
szuserxref
java.lang.String szuserxref
szuserchrom
java.lang.String szuserchrom
ntodownload
int ntodownload
nfdr
int nfdr
balltime
boolean balltime
bspotincluded
boolean bspotincluded
badd0
boolean badd0
bbatchmode
boolean bbatchmode
- True we run in batch mode without a GUI, false we use the GUI
orig1Label
javax.swing.JLabel orig1Label
xrefLabel
javax.swing.JLabel xrefLabel
xrefsourceLabel
javax.swing.JLabel xrefsourceLabel
chromLabel
javax.swing.JLabel chromLabel
categoryIDLabel
javax.swing.JLabel categoryIDLabel
extraLabel
javax.swing.JLabel extraLabel
compare1Label
javax.swing.JLabel compare1Label
compare2Label
javax.swing.JLabel compare2Label
alphaLabel
javax.swing.JLabel alphaLabel
corrmodelLabel
javax.swing.JLabel corrmodelLabel
maxmissingLabel
javax.swing.JLabel maxmissingLabel
filterthresholdLabel
javax.swing.JLabel filterthresholdLabel
expressLabel
javax.swing.JLabel expressLabel
maxchangeLabel
javax.swing.JLabel maxchangeLabel
numberprofilesLabel
javax.swing.JLabel numberprofilesLabel
percentileLabel
javax.swing.JLabel percentileLabel
lbLabel
javax.swing.JLabel lbLabel
samplegeneLabel
javax.swing.JLabel samplegeneLabel
samplemodelLabel
javax.swing.JLabel samplemodelLabel
samplepvalLabel
javax.swing.JLabel samplepvalLabel
goLabel
javax.swing.JLabel goLabel
permuteLabel
javax.swing.JLabel permuteLabel
mingoLabel
javax.swing.JLabel mingoLabel
mingolevelLabel
javax.swing.JLabel mingolevelLabel
randomgoLabel
javax.swing.JLabel randomgoLabel
filterchoiceLabel
javax.swing.JLabel filterchoiceLabel
chromcb
javax.swing.JComboBox chromcb
orgcb
javax.swing.JComboBox orgcb
xrefcb
javax.swing.JComboBox xrefcb
clusteringmethodcb
javax.swing.JComboBox clusteringmethodcb
lognormButton
javax.swing.JRadioButton lognormButton
normButton
javax.swing.JRadioButton normButton
nonormButton
javax.swing.JRadioButton nonormButton
normGroup
javax.swing.ButtonGroup normGroup
chromcheck
javax.swing.JCheckBox chromcheck
anncheck
javax.swing.JCheckBox anncheck
xrefcheck
javax.swing.JCheckBox xrefcheck
obocheck
javax.swing.JCheckBox obocheck
permutecheck
javax.swing.JCheckBox permutecheck
pcheck
javax.swing.JCheckBox pcheck
fcheck
javax.swing.JCheckBox fcheck
ccheck
javax.swing.JCheckBox ccheck
spotcheck
javax.swing.JCheckBox spotcheck
orig1Field
javax.swing.JTextField orig1Field
goField
javax.swing.JTextField goField
chromField
javax.swing.JTextField chromField
extraField
javax.swing.JTextField extraField
xrefField
javax.swing.JTextField xrefField
categoryIDField
javax.swing.JTextField categoryIDField
taxonField
javax.swing.JTextField taxonField
evidenceField
javax.swing.JTextField evidenceField
orig1Button
javax.swing.JButton orig1Button
orig2Button
javax.swing.JButton orig2Button
chromButton
javax.swing.JButton chromButton
goLabelButton
javax.swing.JButton goLabelButton
xrefButton
javax.swing.JButton xrefButton
extraButton
javax.swing.JButton extraButton
categoryIDButton
javax.swing.JButton categoryIDButton
clusterAButton
javax.swing.JButton clusterAButton
logHButton
javax.swing.JButton logHButton
viewButton
javax.swing.JButton viewButton
repeatButton
javax.swing.JButton repeatButton
orig1HButton
javax.swing.JButton orig1HButton
orig2HButton
javax.swing.JButton orig2HButton
advancedHButton
javax.swing.JButton advancedHButton
goLabelHButton
javax.swing.JButton goLabelHButton
categoryIDHButton
javax.swing.JButton categoryIDHButton
extraHButton
javax.swing.JButton extraHButton
numberProfileHButton
javax.swing.JButton numberProfileHButton
changeHButton
javax.swing.JButton changeHButton
maxmissingHButton
javax.swing.JButton maxmissingHButton
filterthresholdHButton
javax.swing.JButton filterthresholdHButton
expressHButton
javax.swing.JButton expressHButton
corrmodelHButton
javax.swing.JButton corrmodelHButton
alphamodelHButton
javax.swing.JButton alphamodelHButton
lbHButton
javax.swing.JButton lbHButton
percentileHButton
javax.swing.JButton percentileHButton
samplegeneHButton
javax.swing.JButton samplegeneHButton
samplemodelHButton
javax.swing.JButton samplemodelHButton
samplepvalHButton
javax.swing.JButton samplepvalHButton
mingoHButton
javax.swing.JButton mingoHButton
mingolevelHButton
javax.swing.JButton mingolevelHButton
methodHButton
javax.swing.JButton methodHButton
xrefsourceHButton
javax.swing.JButton xrefsourceHButton
downloadlistgoHButton
javax.swing.JButton downloadlistgoHButton
xrefHButton
javax.swing.JButton xrefHButton
presetsHButton
javax.swing.JButton presetsHButton
executeHButton
javax.swing.JButton executeHButton
spotHButton
javax.swing.JButton spotHButton
openButton
javax.swing.JButton openButton
infoButton
javax.swing.JButton infoButton
viewHButton
javax.swing.JButton viewHButton
evidenceHButton
javax.swing.JButton evidenceHButton
ontoHButton
javax.swing.JButton ontoHButton
taxonHButton
javax.swing.JButton taxonHButton
randomgoHButton
javax.swing.JButton randomgoHButton
clusteringmethodHButton
javax.swing.JButton clusteringmethodHButton
optionsButton
javax.swing.JButton optionsButton
filterchoiceHButton
javax.swing.JButton filterchoiceHButton
permuteHButton
javax.swing.JButton permuteHButton
chromHButton
javax.swing.JButton chromHButton
chromcbHButton
javax.swing.JButton chromcbHButton
thespinnermingo
javax.swing.JSpinner thespinnermingo
thespinnermingolevel
javax.swing.JSpinner thespinnermingolevel
thespinnerProfile
javax.swing.JSpinner thespinnerProfile
thespinnerChange
javax.swing.JSpinner thespinnerChange
thespinnermaxmissing
javax.swing.JSpinner thespinnermaxmissing
thespinnerfilterthreshold
javax.swing.JSpinner thespinnerfilterthreshold
thespinnerexpress
javax.swing.JSpinner thespinnerexpress
thespinnercorrmodel
javax.swing.JSpinner thespinnercorrmodel
thespinneralpha
javax.swing.JSpinner thespinneralpha
thespinnerlb
javax.swing.JSpinner thespinnerlb
thespinnerpercentile
javax.swing.JSpinner thespinnerpercentile
thespinnersamplegene
javax.swing.JSpinner thespinnersamplegene
thespinnersamplemodel
javax.swing.JSpinner thespinnersamplemodel
thespinnersamplepval
javax.swing.JSpinner thespinnersamplepval
thelogcheck
javax.swing.JCheckBox thelogcheck
theOptions
javax.swing.JDialog theOptions
theRepeatList
ListDialog theRepeatList
szClusterA
java.lang.String szClusterA