Serialized Form


Package org.agmodel.bioinfo.antmap

Class org.agmodel.bioinfo.antmap.AcoParamsBean extends java.lang.Object implements Serializable

serialVersionUID: 1666077872937285707l

Serialized Fields

alpha

double alpha

beta

double beta

rho

double rho

q

double q

n_iteration

int n_iteration

n_ant

int n_ant

init_tau

double init_tau

p_fancy

double p_fancy

weight

double weight

Class org.agmodel.bioinfo.antmap.GroupingOptionBean extends java.lang.Object implements Serializable

serialVersionUID: 1170301808309260031l

Serialized Fields

method

int method

criterion

int criterion

mapFunction

int mapFunction

threshold

double threshold

minNMarker

int minNMarker

Class org.agmodel.bioinfo.antmap.MarkerBean extends java.lang.Object implements Serializable

serialVersionUID: 6414497624917059021l

Serialized Fields

index

int index

Name

java.lang.String Name

location

double location

bootProb

double bootProb

Class org.agmodel.bioinfo.antmap.OrderingOptionBean extends java.lang.Object implements Serializable

serialVersionUID: -3920222151085042694l

Serialized Fields

maxIteration

int maxIteration

nConfirm

int nConfirm

mapFunction

int mapFunction

criterion

int criterion

nBootstrap

int nBootstrap

groupIndex

int groupIndex

Class org.agmodel.bioinfo.antmap.SegDataBean extends java.lang.Object implements Serializable

serialVersionUID: -9011231793710265656l

Serialized Fields

genotypeData

char[][] genotypeData

segType

int segType

markerName

java.lang.String[] markerName

markerType

int[] markerType

Class org.agmodel.bioinfo.antmap.TourBean extends java.lang.Object implements Serializable

serialVersionUID: -1162032944949595017l

Serialized Fields

tourLength

double tourLength

tourOrder

int[] tourOrder


Package org.agmodel.bioinfo.antmapgui

Class org.agmodel.bioinfo.antmapgui.AboutGplDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

borderLayout1

java.awt.BorderLayout borderLayout1

jPanel1

javax.swing.JPanel jPanel1

jButton1

javax.swing.JButton jButton1

jScrollPane1

javax.swing.JScrollPane jScrollPane1

jTextArea1

javax.swing.JTextArea jTextArea1

Class org.agmodel.bioinfo.antmapgui.AcoParamsPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

acoParamsBean

AcoParamsBean acoParamsBean

dppAlpha

DblParamPanel dppAlpha

dppBeta

DblParamPanel dppBeta

dppRho

DblParamPanel dppRho

dppQ

DblParamPanel dppQ

ippNIteration

IntParamPanel ippNIteration

ippNAnt

IntParamPanel ippNAnt

dppInitTau

DblParamPanel dppInitTau

dppPFancy

DblParamPanel dppPFancy

dppWeight

DblParamPanel dppWeight

gridLayout1

java.awt.GridLayout gridLayout1

jPanel1

javax.swing.JPanel jPanel1

jButtonLoad

javax.swing.JButton jButtonLoad

jButtonSave

javax.swing.JButton jButtonSave

jFileChooser1

javax.swing.JFileChooser jFileChooser1

Class org.agmodel.bioinfo.antmapgui.AntMapEngineException extends java.lang.Exception implements Serializable

Class org.agmodel.bioinfo.antmapgui.AntMapOptionPanel extends javax.swing.JTabbedPane implements Serializable

Serialized Fields

groupingOptionPanel

GroupingOptionPanel groupingOptionPanel

orderingOptionPanel

OrderingOptionPanel orderingOptionPanel

acoParamsPanel

AcoParamsPanel acoParamsPanel

drawMapOptionPanel

DrawMapOptionPanel drawMapOptionPanel

Class org.agmodel.bioinfo.antmapgui.ComboBoxPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

text

java.lang.String text

jLabel1

javax.swing.JLabel jLabel1

flowLayout1

java.awt.FlowLayout flowLayout1

jComboBox1

javax.swing.JComboBox jComboBox1

Class org.agmodel.bioinfo.antmapgui.DblParamPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

range

int range

text

java.lang.String text

value

double value

jLabelText

javax.swing.JLabel jLabelText

jLabelValue

javax.swing.JLabel jLabelValue

jTextField

javax.swing.JTextField jTextField

jButtonAlter

javax.swing.JButton jButtonAlter

Class org.agmodel.bioinfo.antmapgui.DrawMapOptionPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

drawMapOptionBean

DrawMapOptionBean drawMapOptionBean

gridLayout1

java.awt.GridLayout gridLayout1

rbpBootstrapProb

RadioButtonPanel rbpBootstrapProb

dppScaleFactor

DblParamPanel dppScaleFactor

ippMapSpacing

IntParamPanel ippMapSpacing

ippMarginSize

IntParamPanel ippMarginSize

fcpGroupName

FontChooserPanel fcpGroupName

fcpMarkerInfo

FontChooserPanel fcpMarkerInfo

Class org.agmodel.bioinfo.antmapgui.DrawMapPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

drawMapOptionBean

DrawMapOptionBean drawMapOptionBean

chromWidth

int chromWidth

tickLength

int tickLength

kinkLength

int kinkLength

spaceLength

int spaceLength

spaceHeight

int spaceHeight

format

java.lang.String format

pWidth

int pWidth

pHeight

int pHeight

bufferedImage

java.awt.image.BufferedImage bufferedImage

gBufferedImage

java.awt.Graphics2D gBufferedImage

Class org.agmodel.bioinfo.antmapgui.FontChooser extends javax.swing.JDialog implements Serializable

Serialized Fields

applied

boolean applied

defaultFont

java.awt.Font defaultFont

panel1

javax.swing.JPanel panel1

gridLayout1

java.awt.GridLayout gridLayout1

ippFontSize

IntParamPanel ippFontSize

cbpFontName

ComboBoxPanel cbpFontName

cbpFontStyle

ComboBoxPanel cbpFontStyle

jPanel1

javax.swing.JPanel jPanel1

jButton_Applly

javax.swing.JButton jButton_Applly

jButton_Cancel

javax.swing.JButton jButton_Cancel

jPanel2

javax.swing.JPanel jPanel2

jTextArea1

javax.swing.JTextArea jTextArea1

jButton_Preview

javax.swing.JButton jButton_Preview

Class org.agmodel.bioinfo.antmapgui.FontChooserPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

font

java.awt.Font font

text

java.lang.String text

flowLayout1

java.awt.FlowLayout flowLayout1

jLabel_Text

javax.swing.JLabel jLabel_Text

jLabel_FontInfo

javax.swing.JLabel jLabel_FontInfo

jButton_Setting

javax.swing.JButton jButton_Setting

Class org.agmodel.bioinfo.antmapgui.GroupingOptionPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

groupingOptionBean

GroupingOptionBean groupingOptionBean

jPanel2

javax.swing.JPanel jPanel2

jLabel2

javax.swing.JLabel jLabel2

jRadioButtonR

javax.swing.JRadioButton jRadioButtonR

jRadioButtonDist

javax.swing.JRadioButton jRadioButtonDist

jRadioButtonP

javax.swing.JRadioButton jRadioButtonP

jRadioButtonLOD

javax.swing.JRadioButton jRadioButtonLOD

buttonGroup1

javax.swing.ButtonGroup buttonGroup1

gridLayout1

java.awt.GridLayout gridLayout1

dppThreshold

DblParamPanel dppThreshold

ippMinNMarker

IntParamPanel ippMinNMarker

rbpMethod

RadioButtonPanel rbpMethod

rbpMapFunction

RadioButtonPanel rbpMapFunction

Class org.agmodel.bioinfo.antmapgui.IntParamPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

range

int range

text

java.lang.String text

value

int value

jLabelText

javax.swing.JLabel jLabelText

jLabelValue

javax.swing.JLabel jLabelValue

jTextField

javax.swing.JTextField jTextField

jButtonAlter

javax.swing.JButton jButtonAlter

Class org.agmodel.bioinfo.antmapgui.MainFrame extends javax.swing.JFrame implements Serializable

Serialized Fields

SI_LOG

int SI_LOG
See Also:
Constant Field Values

SI_DATA

int SI_DATA
See Also:
Constant Field Values

SI_RESULT

int SI_RESULT
See Also:
Constant Field Values

SI_MAP

int SI_MAP
See Also:
Constant Field Values

contentPane

javax.swing.JPanel contentPane

borderLayout1

java.awt.BorderLayout borderLayout1

jMenuBar

javax.swing.JMenuBar jMenuBar

jMenu_File

javax.swing.JMenu jMenu_File

jMenuItem_File_Open

javax.swing.JMenuItem jMenuItem_File_Open

jMenuItem_File_Exit

javax.swing.JMenuItem jMenuItem_File_Exit

jMenu_Save

javax.swing.JMenu jMenu_Save

jMenuItem_Save_Result

javax.swing.JMenuItem jMenuItem_Save_Result

jMenuItem_Save_Log

javax.swing.JMenuItem jMenuItem_Save_Log

jMenu_Anal

javax.swing.JMenu jMenu_Anal

jMenuItem_Anal_Seg

javax.swing.JMenuItem jMenuItem_Anal_Seg

jMenuItem_Anal_Group

javax.swing.JMenuItem jMenuItem_Anal_Group

jMenuItem_Anal_Order

javax.swing.JMenuItem jMenuItem_Anal_Order

jMenuItem_Anal_Boot

javax.swing.JMenuItem jMenuItem_Anal_Boot

jMenuItem_Anal_Full

javax.swing.JMenuItem jMenuItem_Anal_Full

jMenu_Help

javax.swing.JMenu jMenu_Help

jMenuItem_Help_About

javax.swing.JMenuItem jMenuItem_Help_About

jMenuItem_Help_Gpl

javax.swing.JMenuItem jMenuItem_Help_Gpl

jTabbedPane1

javax.swing.JTabbedPane jTabbedPane1

jScrollPane1

javax.swing.JScrollPane jScrollPane1

myTextArea_log

MyTextArea myTextArea_log

jScrollPane2

javax.swing.JScrollPane jScrollPane2

jTextArea_data

javax.swing.JTextArea jTextArea_data

jScrollPane3

javax.swing.JScrollPane jScrollPane3

myTextArea_result

MyTextArea myTextArea_result

jScrollPane4

javax.swing.JScrollPane jScrollPane4

drawMapPanel

DrawMapPanel drawMapPanel

jFileChooser1

javax.swing.JFileChooser jFileChooser1

antMapOptionPanel

AntMapOptionPanel antMapOptionPanel

jSplitPane1

javax.swing.JSplitPane jSplitPane1

jLabel_Status

javax.swing.JLabel jLabel_Status

jProgressBar

javax.swing.JProgressBar jProgressBar

antMapEngine

AntMapEngine antMapEngine

jMenuItem_Anal_Redraw

javax.swing.JMenuItem jMenuItem_Anal_Redraw

jMenuItem_Save_Map

javax.swing.JMenuItem jMenuItem_Save_Map

Class org.agmodel.bioinfo.antmapgui.MyTextArea extends javax.swing.JTextArea implements Serializable

Class org.agmodel.bioinfo.antmapgui.OrderingOptionPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

orderingOptionBean

OrderingOptionBean orderingOptionBean

gridLayout1

java.awt.GridLayout gridLayout1

buttonGroup1

javax.swing.ButtonGroup buttonGroup1

ippNIteration

IntParamPanel ippNIteration

ippNBootstrap

IntParamPanel ippNBootstrap

rbpMapFunction

RadioButtonPanel rbpMapFunction

rbpCriterion

RadioButtonPanel rbpCriterion

cbpTargetedGroup

ComboBoxPanel cbpTargetedGroup

Class org.agmodel.bioinfo.antmapgui.RadioButtonPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

text

java.lang.String text

jLabel1

javax.swing.JLabel jLabel1

buttonGroup

javax.swing.ButtonGroup buttonGroup

buttonList

java.util.ArrayList buttonList


Package org.agmodel.bioinfo.common

Class org.agmodel.bioinfo.common.BisectionBean extends java.lang.Object implements Serializable

serialVersionUID: -5493080134283787024l

Class org.agmodel.bioinfo.common.FileFormatException extends java.lang.Exception implements Serializable

serialVersionUID: -5489997865593004270l


Package org.agmodel.bioinfo.segregation

Class org.agmodel.bioinfo.segregation.FisherInfoForRBean extends java.lang.Object implements Serializable

serialVersionUID: -8079902472884678348l

Class org.agmodel.bioinfo.segregation.RecombinationBean extends java.lang.Object implements Serializable

serialVersionUID: 1319605142840402266l

Serialized Fields

value

double value

n

int n

chi2

double chi2

p

double p

lod

double lod

error

boolean error

Class org.agmodel.bioinfo.segregation.SegRatioBean extends java.lang.Object implements Serializable

serialVersionUID: -8588974661439856657l

Serialized Fields

segType

int segType

markerType

int markerType

n_data

int n_data

n_miss

int n_miss

genotype

char[] genotype

n_obs

int[] n_obs

n_exp

double[] n_exp

chiSqr

double chiSqr

p

double p


Package org.agmodel.bioinfo.stat

Class org.agmodel.bioinfo.stat.MersenneTwister extends java.util.Random implements Serializable

serialVersionUID: 8308633946544548094l

Serialized Fields

x

int[] x

p

int p

q

int q

r

int r