Serialized Form


Package halo.data.dataExceptions

Class halo.data.dataExceptions.InconsistentColumnNumberException extends java.lang.Exception implements Serializable

serialVersionUID: 1967991737081990623L


Package halo.userinterface.cmdline.cmdexceptions

Class halo.userinterface.cmdline.cmdexceptions.InvalidFlagException extends java.lang.Exception implements Serializable

serialVersionUID: 1194462908251849445L

Serialized Fields

flag

java.lang.String flag

Class halo.userinterface.cmdline.cmdexceptions.InvalidMethodException extends java.lang.Exception implements Serializable

serialVersionUID: 1769333775967410986L

Class halo.userinterface.cmdline.cmdexceptions.NoValueException extends java.lang.Exception implements Serializable

serialVersionUID: 3931226977233536492L

Serialized Fields

flag

java.lang.String flag

Package halo.userinterface.gui

Class halo.userinterface.gui.Gui extends javax.swing.JFrame implements Serializable

serialVersionUID: 5557850785265038922L

Serialized Fields

session

Session session

sessName

java.io.File sessName

outputData

java.io.File outputData

outputHL

java.io.File outputHL

pqs

java.io.File pqs

input

java.io.File input

menuLoadSess

javax.swing.JMenuItem menuLoadSess

menuSaveSess

javax.swing.JMenuItem menuSaveSess

menuClearSess

javax.swing.JMenuItem menuClearSess

menuExit

javax.swing.JMenuItem menuExit

menuSaveData

javax.swing.JMenuItem menuSaveData

menuSaveHL

javax.swing.JMenuItem menuSaveHL

menuBias

javax.swing.JMenuItem menuBias

menuSaveR

javax.swing.JMenuItem menuSaveR

menuSaveB

javax.swing.JMenuItem menuSaveB

menuEva

javax.swing.JMenuItem menuEva

menuCalcMed

javax.swing.JMenuItem menuCalcMed

menuMed

javax.swing.JMenuItem menuMed

menuHelpH

javax.swing.JMenuItem menuHelpH

menuHelpAbout

javax.swing.JMenuItem menuHelpAbout

menuHelpWeb

javax.swing.JMenuItem menuHelpWeb

menuSettGene

javax.swing.JMenuItem menuSettGene

menuSettAlpha

javax.swing.JMenuItem menuSettAlpha

menuSettTime

javax.swing.JMenuItem menuSettTime

menuSettR

javax.swing.JMenuItem menuSettR

menuSettMax

javax.swing.JMenuItem menuSettMax

menuSettRep

javax.swing.JMenuItem menuSettRep

menuHelpReplicate

javax.swing.JMenuItem menuHelpReplicate

menuPQS

javax.swing.JMenuItem menuPQS

menuSaveHLA

javax.swing.JMenuItem menuSaveHLA

menuSubSave

javax.swing.JMenuItem menuSubSave

menuNorm

javax.swing.JMenuItem menuNorm

menuCalcHL

javax.swing.JMenuItem menuCalcHL

menuFilter

javax.swing.JMenu menuFilter

menuNormal

javax.swing.JMenu menuNormal

menuHalfLife

javax.swing.JMenu menuHalfLife

methThresh

javax.swing.JRadioButton methThresh

methAbs

javax.swing.JRadioButton methAbs

methPQS

javax.swing.JRadioButton methPQS

methPQSMin

javax.swing.JRadioButton methPQSMin

none

javax.swing.JRadioButton none

dataPa

javax.swing.JPanel dataPa

filtPa

javax.swing.JPanel filtPa

normPa

javax.swing.JPanel normPa

hlPa

javax.swing.JPanel hlPa

corrPa

javax.swing.JPanel corrPa

panel

javax.swing.JPanel panel

sep1

javax.swing.JSeparator sep1

sep2

javax.swing.JSeparator sep2

sep3

javax.swing.JSeparator sep3

filepath

javax.swing.JTextField filepath

chooser

javax.swing.JFileChooser chooser

calc

javax.swing.JButton calc

plotNorm

javax.swing.JButton plotNorm

plotHalf

javax.swing.JButton plotHalf

startHLButton

javax.swing.JButton startHLButton

saveHLs

javax.swing.JButton saveHLs

add

javax.swing.JButton add

c

java.awt.GridBagConstraints c

columnsTotal

java.util.List<E> columnsTotal

columnsNew

java.util.List<E> columnsNew

columnsPre

java.util.List<E> columnsPre

columnsTotalOut

java.util.List<E> columnsTotalOut

columnsNewOut

java.util.List<E> columnsNewOut

columnsPreOut

java.util.List<E> columnsPreOut

attributesOut

java.util.List<E> attributesOut

absenceLabel

java.util.List<E> absenceLabel

attributeFiles

java.util.List<E> attributeFiles

orgLabelsCalls

java.util.List<E> orgLabelsCalls

orgLabelsOther

java.util.List<E> orgLabelsOther

attributeFileLabels

java.util.ArrayList<E> attributeFileLabels

replicates

java.util.List<E> replicates

labels

java.util.ArrayList<E> labels

temporary

java.util.ArrayList<E> temporary

attributesOrg

java.util.ArrayList<E> attributesOrg

attributeLabels

java.util.ArrayList<E> attributeLabels

attributes

java.util.ArrayList<E> attributes

medCorr

java.util.List<E> medCorr

normGraphConstructor

XYGraphConstructor normGraphConstructor

cor

RCorrelationCoefficient cor

loess

RLoessRegression loess

display

java.lang.StringBuffer display

pathR

java.lang.String pathR

spotid

java.lang.String spotid

normMethod

java.lang.String normMethod

uraMeth

java.lang.String uraMeth

method

java.lang.String method

ratioMethod

int ratioMethod

replicate

int replicate

column

int column

startDisplay

int startDisplay

which

int which

tempIndex

int tempIndex

renormalize

boolean renormalize

unequal

boolean unequal

cancel

boolean cancel

corrExpanded

boolean corrExpanded

plotQuality

boolean plotQuality

labelingTime

double labelingTime

medTime

double medTime

median

double median

guiData

GuiFilterData guiData

guiNorm

GuiNormal guiNorm

guiHL

GuiHalfLife guiHL

dataObj

Data dataObj

eval

Normalization eval

alpha

Alpha alpha

Package halo.userinterface.gui.guitools

Class halo.userinterface.gui.guitools.AboutDialog extends javax.swing.JFrame implements Serializable

serialVersionUID: -8007797170913184546L

Serialized Fields

owner

java.awt.Frame owner

Class halo.userinterface.gui.guitools.HelpButton extends javax.swing.JButton implements Serializable

serialVersionUID: -2533991156073064622L

Class halo.userinterface.gui.guitools.InputHelpDialog extends javax.swing.JDialog implements Serializable

serialVersionUID: 4339266350540945367L

Serialized Fields

panel

javax.swing.JPanel panel

field

javax.swing.JTextField field

cancel

boolean cancel

width

int width

height

int height

Class halo.userinterface.gui.guitools.LabelChooserDialog extends javax.swing.JDialog implements Serializable

serialVersionUID: -3181668702954972979L

Serialized Fields

list

java.util.ArrayList<E> list

panel

javax.swing.JPanel panel

cancel

boolean cancel