Serialized Form


Package edu.cmu.cs.sb.chromviewer

Class edu.cmu.cs.sb.chromviewer.ChromEnrichmentTable extends javax.swing.JPanel implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.chromviewer.ChromFrame extends javax.swing.JFrame implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.chromviewer.ChromGeneAcceptTable extends javax.swing.JPanel implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.chromviewer.ChromGeneRejectTable extends javax.swing.JPanel implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.chromviewer.ChromRectangle extends GeneRectangle implements Serializable

Serialized Fields

mChangeLayout

boolean mChangeLayout

gp

GenomeFileParser gp

Class edu.cmu.cs.sb.chromviewer.GeneRectangle extends edu.umd.cs.piccolo.nodes.PPath implements Serializable

Serialized Fields

yp

GenomeFileParser yp

mHorizontalOrientation

boolean mHorizontalOrientation

mGeneInfo

Gene mGeneInfo

mGeneAlias

java.lang.String mGeneAlias

mWidthScale

double mWidthScale

mLeftToRight

boolean mLeftToRight

mInputListener

GeneRectangle.GeneMouseOverHandler mInputListener

Class edu.cmu.cs.sb.chromviewer.TableSorterRoman extends TableSorter implements Serializable

Serialized Fields

nromancol

int nromancol

Package edu.cmu.cs.sb.core

Class edu.cmu.cs.sb.core.DataTable extends javax.swing.JPanel implements Serializable

Serialized Fields

szfile

java.lang.String szfile

Class edu.cmu.cs.sb.core.ListDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.core.MultiLineHeaderRenderer extends javax.swing.JList implements Serializable

Serialized Fields

theTableSorter

TableSorter theTableSorter

Class edu.cmu.cs.sb.core.TableModelSetST extends javax.swing.table.AbstractTableModel implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.core.TableModelST extends javax.swing.table.AbstractTableModel implements Serializable

Serialized Fields

columnNames

java.lang.String[] columnNames
An array of the column header names


data

java.lang.Object[][] data
A multi-dimensional array of data values

Class edu.cmu.cs.sb.core.TableSorter extends javax.swing.table.AbstractTableModel implements Serializable

serialVersionUID: 107L

Serialized Fields

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

Class edu.cmu.cs.sb.drem.DREM_IO extends javax.swing.JFrame implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.drem.DREMGui extends edu.umd.cs.piccolox.PFrame implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.drem.DREMGui_DefineGeneSet extends javax.swing.JPanel implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.drem.DREMGui_EdgeTable extends javax.swing.JPanel implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.drem.DREMGui_FilterGOModel extends javax.swing.table.AbstractTableModel implements Serializable

Serialized Fields

columnNames

java.lang.String[] columnNames
An array of the column header names


data

java.lang.Object[][] data
A multi-dimensional array of data values

Class edu.cmu.cs.sb.drem.DREMGui_FilterStatic extends javax.swing.JPanel implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.drem.DREMGui_FilterStaticModel extends javax.swing.table.AbstractTableModel implements Serializable

Serialized Fields

columnNames

java.lang.String[] columnNames
An array of the column header names


data

java.lang.Object[][] data
A multi-dimensional array of data values

Class edu.cmu.cs.sb.drem.DREMGui_GeneTable extends javax.swing.JPanel implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.drem.DREMGui_GOFilter extends javax.swing.JPanel implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.drem.DREMGui_GOGeneTable extends javax.swing.JPanel implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.drem.DREMGui_GOSplitTable extends javax.swing.JPanel implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.drem.DREMGui_GOTable extends javax.swing.JPanel implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.drem.DREMGui_InterfaceOptions extends javax.swing.JPanel implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.drem.DREMGui_KeyInputs extends javax.swing.JPanel implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.drem.DREMGui_Predict extends javax.swing.JPanel implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.drem.DREMGui_PredictModel extends javax.swing.table.AbstractTableModel implements Serializable

Serialized Fields

columnNames

java.lang.String[] columnNames
An array of the column header names


data

java.lang.Object[][] data
A multi-dimensional array of data values

Class edu.cmu.cs.sb.drem.DREMGui_SaveDREM extends javax.swing.JPanel implements Serializable

Serialized Fields

theDREMGui

DREMGui theDREMGui

validExt

java.util.HashSet<E> validExt

Class edu.cmu.cs.sb.drem.DREMGui_SaveModel extends javax.swing.JPanel implements Serializable

Serialized Fields

theTimeiohmm

DREM_Timeiohmm theTimeiohmm

treecopy

edu.cmu.cs.sb.drem.DREM_Timeiohmm.Treenode treecopy

Class edu.cmu.cs.sb.drem.DREMGui_SplitTable extends javax.swing.JPanel implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.drem.DREMGui_StaticSummaryTable extends javax.swing.JPanel implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.stem.CompareGui extends edu.umd.cs.piccolox.PFrame implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.stem.DefineGeneSet extends javax.swing.JPanel implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.stem.FilteredTable extends javax.swing.JPanel implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.stem.GenePlotPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.stem.GeneTable extends javax.swing.JPanel implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.stem.GOGeneTable extends javax.swing.JPanel implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.stem.GOTable extends javax.swing.JPanel implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.stem.GOTableExpected extends javax.swing.JPanel implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.stem.MAINGUI2 extends edu.umd.cs.piccolox.PFrame implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.stem.MainTable extends javax.swing.JPanel implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.stem.ProfileGui extends javax.swing.JFrame implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.stem.SortTable extends javax.swing.JPanel implements Serializable

Serialized Fields

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

Class edu.cmu.cs.sb.stem.ST extends javax.swing.JFrame implements Serializable

Serialized Fields

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