Serialized Form


Package com.sshtools.common.authentication

Class com.sshtools.common.authentication.AuthenticationDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

jListAuths

javax.swing.JList jListAuths

messageLabel

javax.swing.JLabel messageLabel

cancelled

boolean cancelled

Class com.sshtools.common.authentication.BannerDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

text

javax.swing.JTextArea text

Class com.sshtools.common.authentication.KBIRequestHandlerDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

cancelled

boolean cancelled

instructionLabel

javax.swing.JLabel instructionLabel

buttonsPanel

javax.swing.JPanel buttonsPanel

promptReply

javax.swing.text.JTextComponent[] promptReply

Class com.sshtools.common.authentication.PassphraseDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

jButtonCancel

javax.swing.JButton jButtonCancel

jButtonOK

javax.swing.JButton jButtonOK

message

javax.swing.JLabel message

jPasswordField

javax.swing.JPasswordField jPasswordField

userCancelled

boolean userCancelled

Class com.sshtools.common.authentication.PasswordAuthenticationDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

instance

PasswordAuthenticationClient instance

jButtonCancel

javax.swing.JButton jButtonCancel

jButtonOK

javax.swing.JButton jButtonOK

jPasswordField

javax.swing.JPasswordField jPasswordField

jTextUsername

XTextField jTextUsername

userCancelled

boolean userCancelled

Package com.sshtools.common.automate

Class com.sshtools.common.automate.RemoteIdentificationException extends java.lang.Exception implements Serializable

Class com.sshtools.common.automate.UnsupportedRuleException extends java.lang.Exception implements Serializable


Package com.sshtools.common.configuration

Class com.sshtools.common.configuration.InvalidProfileFileException extends SshException implements Serializable


Package com.sshtools.common.keygen

Class com.sshtools.common.keygen.KeygenPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

browseInput

javax.swing.JButton browseInput

browseOutput

javax.swing.JButton browseOutput

action

javax.swing.JComboBox action

type

javax.swing.JComboBox type

bitsLabel

javax.swing.JLabel bitsLabel

inputFileLabel

javax.swing.JLabel inputFileLabel

newPassphraseLabel

javax.swing.JLabel newPassphraseLabel

oldPassphraseLabel

javax.swing.JLabel oldPassphraseLabel

outputFileLabel

javax.swing.JLabel outputFileLabel

typeLabel

javax.swing.JLabel typeLabel

newPassphrase

javax.swing.JPasswordField newPassphrase

oldPassphrase

javax.swing.JPasswordField oldPassphrase

strength

javax.swing.JProgressBar strength

inputFile

XTextField inputFile

outputFile

XTextField outputFile

bits

NumericTextField bits

Class com.sshtools.common.keygen.KeygenPanel2 extends javax.swing.JPanel implements Serializable

Serialized Fields

browseInput

javax.swing.JButton browseInput

borderLayout1

java.awt.BorderLayout borderLayout1

jPanel1

javax.swing.JPanel jPanel1

key1Panel

javax.swing.JTabbedPane key1Panel

key1GeneratePanel

javax.swing.JPanel key1GeneratePanel

file

javax.swing.JPanel file

borderLayout2

java.awt.BorderLayout borderLayout2

key1DataPanel

javax.swing.JPanel key1DataPanel

jScrollPane1

javax.swing.JScrollPane jScrollPane1

jTextArea1

javax.swing.JTextArea jTextArea1

gridLayout1

java.awt.GridLayout gridLayout1

titledBorder1

javax.swing.border.TitledBorder titledBorder1

titledBorder2

javax.swing.border.TitledBorder titledBorder2

gridBagLayout1

java.awt.GridBagLayout gridBagLayout1

jLabel1

javax.swing.JLabel jLabel1

jTextField1

javax.swing.JTextField jTextField1

jButton1

javax.swing.JButton jButton1

jButton2

javax.swing.JButton jButton2

Class com.sshtools.common.keygen.Main extends javax.swing.JFrame implements Serializable

Serialized Fields

close

javax.swing.JButton close

generate

javax.swing.JButton generate

keygen

KeygenPanel keygen

Package com.sshtools.common.mru

Class com.sshtools.common.mru.MRUAction extends MenuAction implements Serializable

Class com.sshtools.common.mru.MRUList extends java.util.Vector implements Serializable

Serialized Fields

currentElement

java.lang.String currentElement

Class com.sshtools.common.mru.MRUListModel extends javax.swing.AbstractListModel implements Serializable

Serialized Fields

mru

MRUList mru

Class com.sshtools.common.mru.MRUMenu extends javax.swing.JMenu implements Serializable

Serialized Fields

model

MRUListModel model

Package com.sshtools.common.ui

Class com.sshtools.common.ui.AboutAction extends StandardAction implements Serializable

Serialized Fields

application

SshToolsApplication application

parent

java.awt.Component parent

Class com.sshtools.common.ui.BooleanIconRenderer extends javax.swing.table.DefaultTableCellRenderer implements Serializable

Serialized Fields

trueIcon

javax.swing.Icon trueIcon

falseIcon

javax.swing.Icon falseIcon

Class com.sshtools.common.ui.CloseAction extends StandardAction implements Serializable

Class com.sshtools.common.ui.ColorComboBox extends javax.swing.JComboBox implements Serializable

Class com.sshtools.common.ui.ConnectionPropertiesAction extends StandardAction implements Serializable

Class com.sshtools.common.ui.EditAction extends StandardAction implements Serializable

Class com.sshtools.common.ui.ExitAction extends StandardAction implements Serializable

Serialized Fields

application

SshToolsApplication application

container

SshToolsApplicationContainer container

Class com.sshtools.common.ui.FolderBar extends javax.swing.JPanel implements Serializable

Serialized Fields

textLabel

javax.swing.JLabel textLabel

iconLabel

javax.swing.JLabel iconLabel

action

javax.swing.Action action

Class com.sshtools.common.ui.GlobalOptionsTab extends javax.swing.JPanel implements Serializable

Serialized Fields

lafChooser

javax.swing.JComboBox lafChooser

Class com.sshtools.common.ui.HostsTab extends javax.swing.JPanel implements Serializable

Serialized Fields

hosts

javax.swing.JList hosts

hostKeyVerifier

AbstractKnownHostsKeyVerification hostKeyVerifier

remove

javax.swing.JButton remove

model

HostsTab.HostsListModel model

Class com.sshtools.common.ui.IconWrapperPanel extends javax.swing.JPanel implements Serializable

Class com.sshtools.common.ui.ImagePanel extends javax.swing.JPanel implements Serializable

Serialized Fields

icon

ResourceIcon icon

alignBottomRight

boolean alignBottomRight

Class com.sshtools.common.ui.MenuAction extends StandardAction implements Serializable

Class com.sshtools.common.ui.MultilineLabel extends javax.swing.JPanel implements Serializable

Serialized Fields

constraints

java.awt.GridBagConstraints constraints

text

java.lang.String text

Class com.sshtools.common.ui.NewAction extends StandardAction implements Serializable

Class com.sshtools.common.ui.NewWindowAction extends StandardAction implements Serializable

Serialized Fields

log

org.apache.commons.logging.Log log

application

SshToolsApplication application

Class com.sshtools.common.ui.NumericTextField extends XTextField implements Serializable

Serialized Fields

positiveBackground

java.awt.Color positiveBackground

symbols

java.text.DecimalFormatSymbols symbols

numberFormat

java.text.NumberFormat numberFormat

selectAllOnFocusGain

boolean selectAllOnFocusGain

wColumnWidth

int wColumnWidth

Class com.sshtools.common.ui.OpenAction extends StandardAction implements Serializable

Class com.sshtools.common.ui.OptionsAction extends StandardAction implements Serializable

Class com.sshtools.common.ui.OptionsDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

selectedOption

Option selectedOption

callback

OptionCallback callback

defaultButton

javax.swing.JButton defaultButton

Class com.sshtools.common.ui.OptionsPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

log

org.apache.commons.logging.Log log

tabber

Tabber tabber

cancelled

boolean cancelled

Class com.sshtools.common.ui.PrintAction extends StandardAction implements Serializable

Class com.sshtools.common.ui.PrintPreview extends javax.swing.JPanel implements Serializable

Serialized Fields

job

java.awt.print.PrinterJob job

setup

javax.swing.JButton setup

scale

javax.swing.JComboBox scale

pageWidth

int pageWidth

printable

java.awt.print.Printable printable

previewer

PrintPreview.PreviewContainer previewer

pageFormat

java.awt.print.PageFormat pageFormat

pageHeight

int pageHeight

scrollpane

javax.swing.JScrollPane scrollpane

Class com.sshtools.common.ui.PrintPreviewAction extends StandardAction implements Serializable

Class com.sshtools.common.ui.RecordAction extends StandardAction implements Serializable

Class com.sshtools.common.ui.RefreshAction extends StandardAction implements Serializable

Class com.sshtools.common.ui.ResourceIcon extends javax.swing.ImageIcon implements Serializable

Serialized Fields

cls

java.lang.Class<T> cls

Class com.sshtools.common.ui.SaveAction extends StandardAction implements Serializable

Class com.sshtools.common.ui.SaveAsAction extends StandardAction implements Serializable

Class com.sshtools.common.ui.SessionProviderAction extends StandardAction implements Serializable

Serialized Fields

provider

SessionProvider provider

Class com.sshtools.common.ui.SessionProviderFrame extends SshToolsApplicationFrame implements Serializable

Serialized Fields

panel

SshToolsApplicationSessionPanel panel

provider

SessionProvider provider

profile

SshToolsConnectionProfile profile

ssh

SshClient ssh

disconnectOnClose

boolean disconnectOnClose

Class com.sshtools.common.ui.SessionProviderInternalFrame extends SshToolsApplicationInternalFrame implements Serializable

Serialized Fields

panel

SshToolsApplicationSessionPanel panel

provider

SessionProvider provider

profile

SshToolsConnectionProfile profile

ssh

SshClient ssh

disconnectOnClose

boolean disconnectOnClose

Class com.sshtools.common.ui.SshToolsApplicationApplet extends javax.swing.JApplet implements Serializable

Serialized Fields

log

org.apache.commons.logging.Log log

loadingPanel

SshToolsApplicationApplet.LoadingPanel loadingPanel

toolSeparator

javax.swing.JSeparator toolSeparator

applicationPanel

SshToolsApplicationPanel applicationPanel

infoForeground

java.awt.Color infoForeground

infoBorderThickness

int infoBorderThickness

toolBar

boolean toolBar

menuBar

boolean menuBar

statusBar

boolean statusBar

infoBackground

java.awt.Color infoBackground

infoBorderColor

java.awt.Color infoBorderColor

disabledActions

java.lang.String disabledActions

Class com.sshtools.common.ui.SshToolsApplicationApplet.SshToolsApplicationAppletContainer extends javax.swing.JPanel implements Serializable

Serialized Fields

panel

SshToolsApplicationPanel panel

application

SshToolsApplication application

Class com.sshtools.common.ui.SshToolsApplicationClientApplet extends SshToolsApplicationApplet implements Serializable

Serialized Fields

log

org.apache.commons.logging.Log log

connectionProfileLocation

java.lang.String connectionProfileLocation

authenticationMethod

java.lang.String authenticationMethod

host

java.lang.String host

port

int port

user

java.lang.String user

connectImmediately

boolean connectImmediately

showConnectionDialog

boolean showConnectionDialog

disableHostKeyVerification

boolean disableHostKeyVerification

profile

SshToolsConnectionProfile profile

Class com.sshtools.common.ui.SshToolsApplicationClientPanel extends SshToolsApplicationPanel implements Serializable

Serialized Fields

log

org.apache.commons.logging.Log log

hostKeyVerification

HostKeyVerification hostKeyVerification

currentConnectionFile

java.io.File currentConnectionFile

needSave

boolean needSave

currentConnectionProfile

SshToolsConnectionProfile currentConnectionProfile

connectionFileFilter

javax.swing.filechooser.FileFilter connectionFileFilter

ssh

SshClient ssh

Class com.sshtools.common.ui.SshToolsApplicationException extends java.lang.Exception implements Serializable

Class com.sshtools.common.ui.SshToolsApplicationFrame extends javax.swing.JFrame implements Serializable

Serialized Fields

log

org.apache.commons.logging.Log log

exitAction

StandardAction exitAction

aboutAction

StandardAction aboutAction

newWindowAction

StandardAction newWindowAction

toolSeparator

javax.swing.JSeparator toolSeparator

panel

SshToolsApplicationPanel panel

application

SshToolsApplication application

showAboutBox

boolean showAboutBox

showExitAction

boolean showExitAction

showNewWindowAction

boolean showNewWindowAction

showMenu

boolean showMenu

Class com.sshtools.common.ui.SshToolsApplicationInternalFrame extends javax.swing.JInternalFrame implements Serializable

Serialized Fields

log

org.apache.commons.logging.Log log

exitAction

StandardAction exitAction

aboutAction

StandardAction aboutAction

newWindowAction

StandardAction newWindowAction

toolSeparator

javax.swing.JSeparator toolSeparator

panel

SshToolsApplicationPanel panel

application

SshToolsApplication application

showAboutBox

boolean showAboutBox

showExitAction

boolean showExitAction

showNewWindowAction

boolean showNewWindowAction

showMenu

boolean showMenu

Class com.sshtools.common.ui.SshToolsApplicationPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

log

org.apache.commons.logging.Log log

application

SshToolsApplication application

menuBar

javax.swing.JMenuBar menuBar

toolBar

javax.swing.JToolBar toolBar

contextMenu

javax.swing.JPopupMenu contextMenu

container

SshToolsApplicationContainer container

actions

java.util.Vector<E> actions

actionsVisible

java.util.HashMap<K,V> actionsVisible

toolsVisible

boolean toolsVisible

actionMenus

java.util.Vector<E> actionMenus

Class com.sshtools.common.ui.SshToolsApplicationSessionPanel extends SshToolsApplicationPanel implements Serializable

Serialized Fields

log

org.apache.commons.logging.Log log

currentConnectionProfile

SshToolsConnectionProfile currentConnectionProfile

manager

SessionManager manager

Class com.sshtools.common.ui.SshToolsConnectionHostTab extends javax.swing.JPanel implements Serializable

Serialized Fields

jTextHostname

XTextField jTextHostname

jTextPort

NumericTextField jTextPort

jTextUsername

XTextField jTextUsername

jListAuths

javax.swing.JList jListAuths

methods

java.util.List<E> methods

profile

SshToolsConnectionProfile profile

allowAgentForwarding

javax.swing.JCheckBox allowAgentForwarding

log

org.apache.commons.logging.Log log

Class com.sshtools.common.ui.SshToolsConnectionPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

log

org.apache.commons.logging.Log log

tabber

Tabber tabber

profile

SshToolsConnectionProfile profile

Class com.sshtools.common.ui.SshToolsConnectionProtocolTab extends javax.swing.JPanel implements Serializable

Serialized Fields

jComboCipherCS

javax.swing.JComboBox jComboCipherCS

jComboCipherSC

javax.swing.JComboBox jComboCipherSC

jComboMacCS

javax.swing.JComboBox jComboMacCS

jComboMacSC

javax.swing.JComboBox jComboMacSC

jComboCompCS

javax.swing.JComboBox jComboCompCS

jComboCompSC

javax.swing.JComboBox jComboCompSC

jComboKex

javax.swing.JComboBox jComboKex

jComboPK

javax.swing.JComboBox jComboPK

profile

SshToolsConnectionProfile profile

Class com.sshtools.common.ui.SshToolsConnectionProxyTab extends javax.swing.JPanel implements Serializable

Serialized Fields

noProxy

javax.swing.JRadioButton noProxy

httpProxy

javax.swing.JRadioButton httpProxy

socks4Proxy

javax.swing.JRadioButton socks4Proxy

socks5Proxy

javax.swing.JRadioButton socks5Proxy

group

javax.swing.ButtonGroup group

proxyframe

javax.swing.JPanel proxyframe

username

javax.swing.JTextField username

password

javax.swing.JPasswordField password

proxy

javax.swing.JTextField proxy

port

NumericTextField port

profile

SshToolsConnectionProfile profile

log

org.apache.commons.logging.Log log

Class com.sshtools.common.ui.StandardAction extends javax.swing.AbstractAction implements Serializable

Serialized Fields

listeners

javax.swing.event.EventListenerList listeners

Class com.sshtools.common.ui.StartStopStateRenderer extends javax.swing.table.DefaultTableCellRenderer implements Serializable

Serialized Fields

startedIcon

javax.swing.Icon startedIcon

stoppedIcon

javax.swing.Icon stoppedIcon

failedIcon

javax.swing.Icon failedIcon

errorMsg

java.lang.String errorMsg

Class com.sshtools.common.ui.StatusBar extends javax.swing.JPanel implements Serializable

Serialized Fields

connected

StatusBar.StatusLabel connected

statusText

StatusBar.StatusLabel statusText

host

StatusBar.StatusLabel host

user

StatusBar.StatusLabel user

rid

StatusBar.StatusLabel rid

sending

javax.swing.JLabel sending

receiving

javax.swing.JLabel receiving

sendingTimer

javax.swing.Timer sendingTimer

receivingTimer

javax.swing.Timer receivingTimer

Class com.sshtools.common.ui.StopAction extends StandardAction implements Serializable

Class com.sshtools.common.ui.Tabber extends javax.swing.JTabbedPane implements Serializable

Class com.sshtools.common.ui.TextBox extends javax.swing.JTextArea implements Serializable

Serialized Fields

text

java.lang.String text

Class com.sshtools.common.ui.ToolBarSeparator extends javax.swing.JSeparator implements Serializable

Class com.sshtools.common.ui.ToolButton extends javax.swing.JButton implements Serializable

Serialized Fields

hideText

boolean hideText

Class com.sshtools.common.ui.ToolToggleButton extends javax.swing.JToggleButton implements Serializable

Serialized Fields

hideText

boolean hideText

Class com.sshtools.common.ui.XTextField extends javax.swing.JTextField implements Serializable

Serialized Fields

popup

javax.swing.JPopupMenu popup

cutAction

javax.swing.Action cutAction

copyAction

javax.swing.Action copyAction

pasteAction

javax.swing.Action pasteAction

deleteAction

javax.swing.Action deleteAction

selectAllAction

javax.swing.Action selectAllAction

Package com.sshtools.common.util

Class com.sshtools.common.util.UIDException extends java.lang.Exception implements Serializable


Package com.sshtools.daemon.platform

Class com.sshtools.daemon.platform.InvalidHandleException extends java.lang.Exception implements Serializable

Class com.sshtools.daemon.platform.PasswordChangeException extends java.lang.Exception implements Serializable

Class com.sshtools.daemon.platform.PermissionDeniedException extends java.lang.Exception implements Serializable

Class com.sshtools.daemon.platform.UnsupportedFileOperationException extends java.lang.Exception implements Serializable


Package com.sshtools.daemon.terminal

Class com.sshtools.daemon.terminal.BufferOverflowException extends java.lang.Exception implements Serializable


Package com.sshtools.daemon.util

Class com.sshtools.daemon.util.StringPattern extends java.lang.Object implements Serializable

Serialized Fields

ignoreCase

boolean ignoreCase

pattern

java.lang.String pattern

digitWildcard

java.lang.Character digitWildcard

Package com.sshtools.j2ssh

Class com.sshtools.j2ssh.SshException extends java.io.IOException implements Serializable

Class com.sshtools.j2ssh.SshRuntimeException extends java.lang.RuntimeException implements Serializable

Class com.sshtools.j2ssh.TransferCancelledException extends java.io.IOException implements Serializable


Package com.sshtools.j2ssh.agent

Class com.sshtools.j2ssh.agent.AgentNotAvailableException extends java.lang.Exception implements Serializable

Class com.sshtools.j2ssh.agent.KeyTimeoutException extends java.lang.Exception implements Serializable


Package com.sshtools.j2ssh.authentication

Class com.sshtools.j2ssh.authentication.AuthenticationProtocolException extends java.io.IOException implements Serializable

Class com.sshtools.j2ssh.authentication.TerminatedStateException extends java.lang.Exception implements Serializable

Serialized Fields

state

int state

Package com.sshtools.j2ssh.configuration

Class com.sshtools.j2ssh.configuration.ConfigurationException extends SshException implements Serializable


Package com.sshtools.j2ssh.connection

Class com.sshtools.j2ssh.connection.ChannelState extends State implements Serializable

Class com.sshtools.j2ssh.connection.InvalidChannelException extends java.io.IOException implements Serializable


Package com.sshtools.j2ssh.forwarding

Class com.sshtools.j2ssh.forwarding.ForwardingConfigurationException extends java.io.IOException implements Serializable


Package com.sshtools.j2ssh.io

Class com.sshtools.j2ssh.io.IOStreamConnectorState extends State implements Serializable

Class com.sshtools.j2ssh.io.UnsignedInteger32 extends java.lang.Number implements Serializable

serialVersionUID: 200L

Serialized Fields

value

java.lang.Long value

Class com.sshtools.j2ssh.io.UnsignedInteger64 extends java.lang.Number implements Serializable

serialVersionUID: 200L

Serialized Fields

bigInt

java.math.BigInteger bigInt

Package com.sshtools.j2ssh.transport

Class com.sshtools.j2ssh.transport.AlgorithmInitializationException extends TransportProtocolException implements Serializable

Class com.sshtools.j2ssh.transport.AlgorithmNotAgreedException extends TransportProtocolException implements Serializable

Class com.sshtools.j2ssh.transport.AlgorithmNotSupportedException extends TransportProtocolException implements Serializable

Class com.sshtools.j2ssh.transport.AlgorithmOperationException extends TransportProtocolException implements Serializable

Class com.sshtools.j2ssh.transport.InvalidHostFileException extends TransportProtocolException implements Serializable

Class com.sshtools.j2ssh.transport.InvalidMessageException extends TransportProtocolException implements Serializable

Class com.sshtools.j2ssh.transport.MessageAlreadyRegisteredException extends SshException implements Serializable

Class com.sshtools.j2ssh.transport.MessageNotAvailableException extends java.lang.Exception implements Serializable

Class com.sshtools.j2ssh.transport.MessageNotRegisteredException extends SshException implements Serializable

Class com.sshtools.j2ssh.transport.MessageStoreEOFException extends TransportProtocolException implements Serializable

Class com.sshtools.j2ssh.transport.ServiceState extends State implements Serializable

Class com.sshtools.j2ssh.transport.TransportProtocolException extends SshException implements Serializable

Class com.sshtools.j2ssh.transport.TransportProtocolState extends State implements Serializable

Serialized Fields

lastError

java.io.IOException lastError

reason

java.lang.String reason

Package com.sshtools.j2ssh.transport.kex

Class com.sshtools.j2ssh.transport.kex.KeyExchangeException extends TransportProtocolException implements Serializable


Package com.sshtools.j2ssh.transport.publickey

Class com.sshtools.j2ssh.transport.publickey.InvalidSshKeyException extends TransportProtocolException implements Serializable

Class com.sshtools.j2ssh.transport.publickey.InvalidSshKeySignatureException extends TransportProtocolException implements Serializable


Package com.sshtools.j2ssh.util

Class com.sshtools.j2ssh.util.InvalidStateException extends java.lang.RuntimeException implements Serializable

Class com.sshtools.j2ssh.util.OpenClosedState extends State implements Serializable

Class com.sshtools.j2ssh.util.StartStopState extends State implements Serializable

Class com.sshtools.j2ssh.util.State extends java.lang.Object implements Serializable

Serialized Fields

state

int state

Package edu.harvard.mgh.purcell.gCLINE

Class edu.harvard.mgh.purcell.gCLINE.DeleteOpDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

operations

javax.swing.JCheckBox[] operations
A JCheckBox array that holds the deletion options for the selected opertaions.


outfiles

java.util.Vector<E> outfiles
A JCheckBox array that holds the deletion options for the selected output files.


infiles

java.util.Vector<E> infiles
A JCheckBox array that holds the deletion options for the selected input files.


data

Record data
The Record that the operations are attached to.


deleteFileOp

java.awt.event.ActionListener deleteFileOp
An ActionListener that deletes the files and operations that are selected in the check boxes.

Class edu.harvard.mgh.purcell.gCLINE.EditFolderDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

frame

StartFrame frame

data

Record data

filePanel

javax.swing.JPanel filePanel

buttonPanel

javax.swing.JPanel buttonPanel

fileLabels

javax.swing.JLabel[] fileLabels

fileDisc

javax.swing.JTextField[] fileDisc

names

java.lang.String[] names

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

close

java.awt.event.ActionListener close

setDisc

java.awt.event.ActionListener setDisc

Class edu.harvard.mgh.purcell.gCLINE.EditOpDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

data

Record data

discLabel

javax.swing.JLabel discLabel

discText

javax.swing.JTextField discText

clineText

javax.swing.JTextArea clineText

infileLabel

javax.swing.JLabel[] infileLabel

outfileLabel

javax.swing.JLabel[] outfileLabel

infileText

javax.swing.JTextField[] infileText

outfileText

javax.swing.JTextField[] outfileText

input

javax.swing.JPanel input

output

javax.swing.JPanel output

buttons

javax.swing.JPanel buttons

command

javax.swing.JScrollPane command

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

oldname

java.lang.String oldname

time

java.lang.String time

numInfile

int numInfile

numOutfile

int numOutfile

replaceOp

java.awt.event.ActionListener replaceOp

closeDialog

java.awt.event.ActionListener closeDialog

Class edu.harvard.mgh.purcell.gCLINE.HierarchyDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

ancesters

javax.swing.JTree ancesters

decendents

javax.swing.JTree decendents

data

Record data

opName

java.lang.String opName

fileName

java.lang.String fileName

Class edu.harvard.mgh.purcell.gCLINE.LinkNewFileDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

data

Record data
A Record that this operation is stored in.


opName

java.lang.String opName
A String that identifies the operation you want to link the file to.


addFile

javax.swing.JTextField addFile
A JTextField that holds the file name.


infile

javax.swing.JRadioButton infile
A JRadioButton that flags this as an input file.


process

java.awt.event.ActionListener process
The ActionListener that adds the file to the operation. If there is nothing in the text field then it does nothng.


cancel

java.awt.event.ActionListener cancel
An ActionListener that closes the dialog without doing anything.

Class edu.harvard.mgh.purcell.gCLINE.PopUpMenu extends javax.swing.JPopupMenu implements Serializable

Serialized Fields

localFilenames

java.lang.String[] localFilenames
An array of the full file names of selected local files


remoteFilenames

java.lang.String[] remoteFilenames
An array of the full file names of selected remote files


fileNames

java.lang.String[] fileNames

opnames

java.lang.String[] opnames
An array of the operation names


frame

StartFrame frame
A StartFrame this menu is attached to


data

Record data
The Record this menu is attached to


download

java.awt.event.ActionListener download
Download selected files


openAlt

java.awt.event.ActionListener openAlt
Launch the user specified file viewer.


openDefault

java.awt.event.ActionListener openDefault
Launch the default file viewer


showHierachyOp

java.awt.event.ActionListener showHierachyOp

showHierachyFile

java.awt.event.ActionListener showHierachyFile

editOp

java.awt.event.ActionListener editOp

editFile

java.awt.event.ActionListener editFile

deleteOp

java.awt.event.ActionListener deleteOp

addFileToOp

java.awt.event.ActionListener addFileToOp

removeFileFromOp

java.awt.event.ActionListener removeFileFromOp

Class edu.harvard.mgh.purcell.gCLINE.RestoreDataDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

logger

org.apache.log4j.Logger logger
A logger for this class


fileField

javax.swing.JTextField fileField

localChooser

GCFileChooser localChooser

data

Record data

Class edu.harvard.mgh.purcell.gCLINE.StartFrame extends javax.swing.JFrame implements Serializable

Serialized Fields

fileViewer

FileView fileViewer
A panel that views the associated log files.


folderViewer

FolderView folderViewer
A panel to view the files in your project folder.


opViewer

OpView opViewer
A panel to look at the operation tree.


version

java.lang.String version
The version number assocated with this gui.


messanger

ErrorManager messanger
The error manager for this gui.


statusBar

javax.swing.JLabel statusBar
A label that informs weather files are in transit from or to a remote directory, this is shown at the lower right hand side.


filesInTransit

java.util.Vector<E> filesInTransit
A Vector that stores the files currently being transmited.


closing

java.awt.event.ActionListener closing
An ActionListener that closers the gui.


properClosing

java.awt.event.WindowListener properClosing
A WindowListener that closes the gui properly.


isBrowseOnly

boolean isBrowseOnly

Package edu.harvard.mgh.purcell.gCLINE.data

Class edu.harvard.mgh.purcell.gCLINE.data.AutoUpdater.MyRenderer extends javax.swing.tree.DefaultTreeCellRenderer implements Serializable

Serialized Fields

sucessIcon

javax.swing.Icon sucessIcon

failIcon

javax.swing.Icon failIcon

runningIcon

javax.swing.Icon runningIcon

fileInfoIcon

javax.swing.Icon fileInfoIcon

Class edu.harvard.mgh.purcell.gCLINE.data.FileInfo extends javax.swing.tree.DefaultMutableTreeNode implements Serializable

Serialized Fields

filename

java.lang.String filename
A string that holds the absolute file name.


globalDisc

java.lang.String globalDisc
A string that holds the global discrition of this file.


localDisc

java.lang.String localDisc
A string that holds an operation specific discription of this file.

Class edu.harvard.mgh.purcell.gCLINE.data.OperationInfo extends javax.swing.tree.DefaultMutableTreeNode implements Serializable

Serialized Fields

name

java.lang.String name
A String that uniquely identifies the operation.


discription

java.lang.String discription
A String that discribes the operation.


cline

java.lang.String cline
A String that holds the command line for this operation.


input

javax.swing.tree.DefaultMutableTreeNode input
A DefaultMutableTreeName that holds the input files.


output

javax.swing.tree.DefaultMutableTreeNode output
A DefaultMutableTreeNode that holds the output files.


timestamp

java.lang.String timestamp

Class edu.harvard.mgh.purcell.gCLINE.data.Record extends javax.swing.tree.DefaultTreeModel implements Serializable

Serialized Fields

OP_LOG_EXT

java.lang.String OP_LOG_EXT
A string that identifies the file extention for the operation log file. Note that this can be changed by the user


frame

StartFrame frame
A JFrame that holds the main GUI


remoteConfig

java.util.Properties remoteConfig
Holds the information for the remote connection. populated from info including: user name, host name, port number, remote project folder name


globalConfig

java.util.Properties globalConfig
Holds the global configuration data. Includes: Alternative editor


localConfig

java.util.Properties localConfig
Holds the local project configuration data. Includes: local project folder name, home folder name


isNew

boolean isNew

globalFileNotes

java.util.HashMap<K,V> globalFileNotes
A HashMap that carries the global file notes


myLock

Lock myLock
Locking information for the folder


conn

SshClient conn
A String that holds the ssh connection.


update

AutoUpdater update
Automatically checks the home directory for new files and updates the displays.


Package edu.harvard.mgh.purcell.gCLINE.general

Class edu.harvard.mgh.purcell.gCLINE.general.Configure extends javax.swing.JDialog implements Serializable

Serialized Fields

data

Record data
Access


localChooser

GCFileChooser localChooser

editor

javax.swing.JTextField editor

updateField

javax.swing.JTextField updateField

Class edu.harvard.mgh.purcell.gCLINE.general.GCFileChooser.FileChoosenEvent extends java.util.EventObject implements Serializable


Package edu.harvard.mgh.purcell.gCLINE.pane

Class edu.harvard.mgh.purcell.gCLINE.pane.FileView extends javax.swing.JPanel implements Serializable

Serialized Fields

textdisplay

javax.swing.JTextArea textdisplay

currentFile

javax.swing.JLabel currentFile

Package edu.harvard.mgh.purcell.gCLINE.tester

Class edu.harvard.mgh.purcell.gCLINE.tester.MenuBarMain extends javax.swing.JMenuBar implements Serializable

Serialized Fields

parent

TestFrame parent

myConfig

Configure myConfig

project1

java.lang.String project1

project2

java.lang.String project2

project3

java.lang.String project3

project4

java.lang.String project4

Class edu.harvard.mgh.purcell.gCLINE.tester.Open extends javax.swing.JDialog implements Serializable

Serialized Fields

logger

org.apache.log4j.Logger logger
A logger for this clas


parent

TestFrame parent
The main frame of the program.


localChooser

GCFileChooser localChooser
Our file choosing class for the local directory.


remoteChooser

GCFileChooser remoteChooser
Our file choosing class for the remote directory.


localProject

javax.swing.JTextField localProject
Let the user look at the local project directory.


remoteProject

javax.swing.JTextField remoteProject
Let the user look at the remote project directory


host

javax.swing.JTextField host

user

javax.swing.JTextField user

port

javax.swing.JTextField port

conn

SshClient conn

data

TestFrame.myProject data

remoteFlag

javax.swing.JCheckBox remoteFlag
Let the user flag this project as remote.


remotePanel

javax.swing.JPanel remotePanel
A panel containing all the fields pertinate to the remote directory.

Class edu.harvard.mgh.purcell.gCLINE.tester.TestFrame extends StartFrame implements Serializable

Serialized Fields

data

TestFrame.myProject data

Package edu.harvard.mgh.purcell.gPLINK2

Class edu.harvard.mgh.purcell.gPLINK2.AddGenericOp extends javax.swing.JDialog implements Serializable

Serialized Fields

data

Project data
The project that this dialog adds the operation to.


allOps

java.util.Vector<E> allOps
A vector of strings that contain all the operation names


opName

javax.swing.JTextField opName
The JTextField that holds the operation name


opDisc

javax.swing.JTextField opDisc
The JTextField that holds the operation discription


tempIn

javax.swing.JTextField tempIn
The JTextField that holds an input file. This field is not actually show to the user


tempOut

javax.swing.JTextField tempOut
The JTextField that holds the new output file. This field is not actually shown to the user


cline

javax.swing.JTextField cline
The JTextField that holds the commandline


infiles

javax.swing.JList infiles
A list that holds all the current inputfiles


inlistmodel

javax.swing.DefaultListModel inlistmodel
A DefaultListModel that holds the data for the input list.


outfiles

javax.swing.JList outfiles
A list that holds all the current output files


outlistmodel

javax.swing.DefaultListModel outlistmodel
A DefaultListModel that holds the data for the output list


addIn

AddGenericOp.BrowseButton addIn
pickAFileButton that browse to select the input files


addOut

AddGenericOp.BrowseButton addOut
pickAFileButton that browse to select the output files


ok

javax.swing.JButton ok
A JButton that signals the form is complete


cancel

javax.swing.JButton cancel
A JButton that signals the cancelation of the form.


processIn

javax.swing.event.DocumentListener processIn
Listen to the temperary JTextField for input file to add to the operation.


processOut

javax.swing.event.DocumentListener processOut
Listen to the temperary JTextField for the output file to add to the operation


validateForm

javax.swing.event.DocumentListener validateForm
Once there is a unique operation name the ok button is enabled.


closeForm

java.awt.event.ActionListener closeForm
Close everything up nicely


addOp

java.awt.event.ActionListener addOp
Add the operation to the project

Class edu.harvard.mgh.purcell.gPLINK2.AddGenericOp.BrowseButton extends javax.swing.JButton implements Serializable

Serialized Fields

target

javax.swing.JTextField target

pick

GCFileChooser pick

Class edu.harvard.mgh.purcell.gPLINK2.GPLINK extends StartFrame implements Serializable

Serialized Fields

data

Project data
The current project we are looking at.


menu

PlinkMenuBar menu

properClosing

java.awt.event.WindowListener properClosing
Create a windowListener that will properly close this class.

Class edu.harvard.mgh.purcell.gPLINK2.OpenHapDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

frame

GPLINK frame
The GPLINK instance this dialog is attached to. We access the project data through this.


pedInfoRB

javax.swing.JRadioButton pedInfoRB
A JRadioButton to flag the ped/info file option for haploview


pedFile

javax.swing.JTextField pedFile
A JTextField that holds the full ped file path.


pedButton

javax.swing.JButton pedButton
A JButton that triggers the ped file browse.


infoFile

javax.swing.JTextField infoFile
A JTextField that holds the full info file path.


infoButton

javax.swing.JButton infoButton
A JButton that triggers the info file browse.


nonSNPRB

javax.swing.JRadioButton nonSNPRB
A JRadioButton to flag the nonSNP file option. This is the default option for a random file.


nonSNPFile

javax.swing.JTextField nonSNPFile
A JTextField that holds the full path name of nonSNP reconized files. This is the default.


nonSNPButton

javax.swing.JButton nonSNPButton
A JButton that browses for the nonSNP file.


SNPRB

javax.swing.JRadioButton SNPRB
A JRadioButton to flag the SNP file option


SNPFile

javax.swing.JTextField SNPFile
A JTextField that holds a SNP defined file name.


SNPButton

javax.swing.JButton SNPButton
A JButton to browse for SNP defined files.


mapFile

javax.swing.JTextField mapFile
A JTextField that holds the map/bim file names.


mapButton

javax.swing.JButton mapButton
A JButton that triggers a browse for the map/bim file.


ok

javax.swing.JButton ok
A JButton that signals to process and close the dialog.


cancel

javax.swing.JButton cancel
A JButton to close the dialog without doing anything.


setFields

java.awt.event.ItemListener setFields
An ItemListener to set the JTextFields and JButtons to reflect the corrisponding radio button selection.


openHaplo

java.awt.event.ActionListener openHaplo
An ActionListener that attaches to the ok button and opens an instance of haploview using the files specified in the dialog.

Class edu.harvard.mgh.purcell.gPLINK2.PLINK_Config extends Configure implements Serializable

Serialized Fields

plinkPath

javax.swing.JTextField plinkPath
A JTextField for the plink path.


plinkPrefix

javax.swing.JTextField plinkPrefix
A JTextField for the plink prefix command.


haploPath

javax.swing.JTextField haploPath
A JTextField for the haploview jar path.


haploAppend

javax.swing.JTextField haploAppend
A JTextField for the haploview append command.


data

Project data
The project we are configuring.


frame

GPLINK frame

Class edu.harvard.mgh.purcell.gPLINK2.PLINK_Execute extends javax.swing.JDialog implements Serializable

Serialized Fields

command

javax.swing.JTextField command
A JTextField that holds the command we wish to pass to the computer.


discription

javax.swing.JTextField discription
A JTextField that holds the discription of the operation.


frame

GPLINK frame
The GPLINK instance we want to store the operation in.

Class edu.harvard.mgh.purcell.gPLINK2.PLINK_Import extends javax.swing.JDialog implements Serializable

Serialized Fields

logger

org.apache.log4j.Logger logger
A logger for this class


frame

StartFrame frame
The StartFrame that this dialog is attached to.


data

Project data
The Project that the operation is added to.


nonincludedRoots

javax.swing.JComboBox nonincludedRoots
A combo box that contains all the log file roots that are not already in the operation tree.


allBox

javax.swing.JCheckBox allBox
A JCheckBox that flags selection of all the non-included roots.


finalLogRoots

java.util.Vector<E> finalLogRoots
A Vector that holds all non-included roots

Class edu.harvard.mgh.purcell.gPLINK2.PLINK_Open extends javax.swing.JDialog implements Serializable

Serialized Fields

logger

org.apache.log4j.Logger logger
A logger for this class


parent

GPLINK parent
The JFrame of the program.


localChooser

GCFileChooser localChooser
Our file choosing class for the local directory.


remoteBrowse

javax.swing.JButton remoteBrowse

remoteChooser

GCFileChooser remoteChooser
Our file choosing class for the remote directory.


localProject

javax.swing.JTextField localProject
Let the user look at the local project directory.


remoteProject

javax.swing.JTextField remoteProject
Let the user look at the remote project directory


host

javax.swing.JTextField host
A JTextField that keeps the host name.


user

javax.swing.JTextField user
A JTextField that keeps the user name.


port

javax.swing.JTextField port
A JTextField that keeps the port number as a string.


conn

SshClient conn
A SshClient that is used to open the remote browser.


remoteFlag

javax.swing.JCheckBox remoteFlag
Let the user flag this project as remote.


ok

javax.swing.JButton ok

remotePanel

javax.swing.JPanel remotePanel
A panel containing all the fields pertinate to the remote directory.

Class edu.harvard.mgh.purcell.gPLINK2.PlinkMenuBar extends javax.swing.JMenuBar implements Serializable

Serialized Fields

logger

org.apache.log4j.Logger logger
A logger for this class


data

Project data
A Project that we are going to pass ...to the form dialogs.


frame

GPLINK frame
A GPLINK that this menu bar is attached to.


project1

java.lang.String project1
A String holding the most recent project that have been opened.


project2

java.lang.String project2
A String holding the second most recent project that have been opened.


project3

java.lang.String project3
A String holding the third most recent project that have been opened.


project4

java.lang.String project4
A String holding the forth most recent project that have been opened.


plink

javax.swing.JMenu plink

config

javax.swing.JMenuItem config

save

javax.swing.JMenuItem save

backup

javax.swing.JMenuItem backup

restore

javax.swing.JMenuItem restore

browse

javax.swing.JCheckBoxMenuItem browse

Package edu.harvard.mgh.purcell.gPLINK2.baseForm

Class edu.harvard.mgh.purcell.gPLINK2.baseForm.FilterDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

parent

Form parent

chrCBox

javax.swing.JComboBox chrCBox

toCBox

javax.swing.JComboBox toCBox

fromCBox

javax.swing.JComboBox fromCBox

eeCBox

javax.swing.JComboBox eeCBox

krCBox

javax.swing.JComboBox krCBox

sexFilterCBox

javax.swing.JComboBox sexFilterCBox

ccFilterCBox

javax.swing.JComboBox ccFilterCBox

fFilterCBox

javax.swing.JComboBox fFilterCBox

setField

javax.swing.JTextField setField

geneField

javax.swing.JTextField geneField

fromField

javax.swing.JTextField fromField

toField

javax.swing.JTextField toField

SNPField

javax.swing.JTextField SNPField

windowField

javax.swing.JTextField windowField

eeField

javax.swing.JTextField eeField

krField

javax.swing.JTextField krField

filterFileField

javax.swing.JTextField filterFileField

filterKeyField

javax.swing.JTextField filterKeyField

mfilterField

javax.swing.JTextField mfilterField

chrButton

javax.swing.JCheckBox chrButton

sgButton

javax.swing.JCheckBox sgButton

ftButton

javax.swing.JCheckBox ftButton

swButton

javax.swing.JCheckBox swButton

eeButton

javax.swing.JCheckBox eeButton

krButton

javax.swing.JCheckBox krButton

fileFilterButton

javax.swing.JCheckBox fileFilterButton

sexFilterButton

javax.swing.JCheckBox sexFilterButton

ccFilterButton

javax.swing.JCheckBox ccFilterButton

fFilterButton

javax.swing.JCheckBox fFilterButton

setButton

FilterDialog.BrowseButton setButton

eeBrowse

FilterDialog.BrowseButton eeBrowse

krBrowse

FilterDialog.BrowseButton krBrowse

filterBrowse

FilterDialog.BrowseButton filterBrowse

okButton

javax.swing.JButton okButton

cancelButton

javax.swing.JButton cancelButton

geneLable

javax.swing.JLabel geneLable

toLabel

javax.swing.JLabel toLabel

wLabel

javax.swing.JLabel wLabel

lengthOpt1

java.lang.String[] lengthOpt1

lengthOpt2

java.lang.String[] lengthOpt2

pickMap

java.awt.event.ActionListener pickMap

pickList

java.awt.event.ActionListener pickList

pickFilter

java.awt.event.ActionListener pickFilter

changeFromTo

java.awt.event.ItemListener changeFromTo

properClosing

java.awt.event.WindowListener properClosing

cancel

java.awt.event.ActionListener cancel

process

java.awt.event.ActionListener process

Class edu.harvard.mgh.purcell.gPLINK2.baseForm.FilterDialog.BrowseButton extends javax.swing.JButton implements Serializable

Serialized Fields

suffex

java.lang.String suffex

suffexDisc

java.lang.String suffexDisc

target

javax.swing.JTextField target

pick

GCFileChooser pick

Class edu.harvard.mgh.purcell.gPLINK2.baseForm.Form extends javax.swing.JDialog implements Serializable

Serialized Fields

parent

GPLINK parent
The GPLINK instance that this form is attached to.


input

InputPane input
The InputPane for this form. This is made public so that the merge form can access certain functions.


output

OutputPane output
The OutputPane for this form.


filter

java.lang.String filter

threshold

java.lang.String threshold

validBody

boolean validBody
Flag if the body of the form is filled out correctly.


ok

javax.swing.JButton ok
The ok button on the form, this is a class variable because it is en/disabled in okForm()


cancel

javax.swing.JButton cancel

filterButton

javax.swing.JButton filterButton

thresholdButton

javax.swing.JButton thresholdButton

validateBodyAL

java.awt.event.ActionListener validateBodyAL

validateBodyDL

javax.swing.event.DocumentListener validateBodyDL

Class edu.harvard.mgh.purcell.gPLINK2.baseForm.Form.BrowseButton extends javax.swing.JButton implements Serializable

Serialized Fields

suffex

java.lang.String suffex

suffexDisc

java.lang.String suffexDisc

target

javax.swing.JTextField target

pick

GCFileChooser pick

Class edu.harvard.mgh.purcell.gPLINK2.baseForm.InputPane extends javax.swing.JTabbedPane implements Serializable

Serialized Fields

parent

GPLINK parent
The GPLINK istance this is attached to.


parentForm

Form parentForm
The dialog that we want to attach our file name browsing window to.


validInput

boolean validInput

binCheck

javax.swing.JCheckBox binCheck
A JCheckBox that flags a quick binary input file format (--bfile filename).


binShort

javax.swing.JComboBox binShort
A JComboBox that holds the quick binary file roots


bedField

javax.swing.JTextField bedField
A JTextField that holds the bed file name


bedBrowse

Form.BrowseButton bedBrowse
A BrowseButton that selects the bed file


bimField

javax.swing.JTextField bimField
A JTextField that holds the bim file name.


bimBrowse

Form.BrowseButton bimBrowse
A BrowseButton thta selects the bim file


famField

javax.swing.JTextField famField
A JTextField that holds the fam file name.


famBrowse

Form.BrowseButton famBrowse
A BrowseButton that selects the fam file.


stdCheck

javax.swing.JCheckBox stdCheck
A JCheckBox that flags the short standard input format (--file fileroot)


stdShort

javax.swing.JComboBox stdShort
A JComboBox that holds the file root options for the short standard input format


pedField

javax.swing.JTextField pedField
A JTextField that holds the ped file name


pedBrowse

Form.BrowseButton pedBrowse
A BrowseButton that selects the ped file.


mapField

javax.swing.JTextField mapField
A JTextField that holds the map file name.


mapBrowse

Form.BrowseButton mapBrowse
A BrowseButton that selects the map file.


useAlt

javax.swing.JCheckBox useAlt
A JCheckBox that flags an alternative phenotype


altField

javax.swing.JTextField altField
A JTextField that holds the alternative pheotype file name.


altBrowse

Form.BrowseButton altBrowse
A BrowseButton that selects the alternative pheotype file name.


useColm

javax.swing.JCheckBox useColm
A JCheckBox that adds a column option to the alternative pheontype


mphenoText

javax.swing.JTextField mphenoText
A JTextField that contains the column you wish to use on the alternative pheotype file.


checkFields

javax.swing.event.DocumentListener checkFields

Class edu.harvard.mgh.purcell.gPLINK2.baseForm.OutputPane extends javax.swing.JPanel implements Serializable

Serialized Fields

op_log_ext

java.lang.String op_log_ext
The extention for the operation log files


rootList

java.util.Vector<E> rootList
A Vector of Strings that are the files in the home directory that end with the operation log extention.


root

javax.swing.JTextField root
The proposed output root.


parentForm

Form parentForm
The form this output pane is going to appear in.


validOutput

boolean validOutput
Flag the form as valid or not valid.

Class edu.harvard.mgh.purcell.gPLINK2.baseForm.ThresholdDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

parent

Form parent
The form that this dialog is attached to


maf

javax.swing.JTextField maf
Fields for user entered thresholds


maxMaf

javax.swing.JTextField maxMaf
Fields for user entered thresholds


geno

javax.swing.JTextField geno
Fields for user entered thresholds


mind

javax.swing.JTextField mind
Fields for user entered thresholds


hwe

javax.swing.JTextField hwe
Fields for user entered thresholds


mendell

javax.swing.JTextField mendell
Fields for user entered thresholds


mendell2

javax.swing.JTextField mendell2
Fields for user entered thresholds


mafButton

javax.swing.JCheckBox mafButton
Buttons to flag user specified thresholds


maxMafButton

javax.swing.JCheckBox maxMafButton
Buttons to flag user specified thresholds


genoButton

javax.swing.JCheckBox genoButton
Buttons to flag user specified thresholds


hweButton

javax.swing.JCheckBox hweButton
Buttons to flag user specified thresholds


mendellButton

javax.swing.JCheckBox mendellButton
Buttons to flag user specified thresholds


mindButton

javax.swing.JCheckBox mindButton
Buttons to flag user specified thresholds


okButton

javax.swing.JButton okButton
Buttons to operate this dialog


resetButton

javax.swing.JButton resetButton
Buttons to operate this dialog


cancelButton

javax.swing.JButton cancelButton
Buttons to operate this dialog


properClosing

java.awt.event.WindowListener properClosing

process

java.awt.event.ActionListener process
Process the dialog to command line.


reset

java.awt.event.ActionListener reset
Reset all the defaults


cancel

java.awt.event.ActionListener cancel
Cancel the dailog and throw it away without changing things


Package edu.harvard.mgh.purcell.gPLINK2.data

Class edu.harvard.mgh.purcell.gPLINK2.data.Project extends Record implements Serializable


Package edu.harvard.mgh.purcell.gPLINK2.forms

Class edu.harvard.mgh.purcell.gPLINK2.forms.AlleleAssoc extends Form implements Serializable

Serialized Fields

permButton

javax.swing.JCheckBox permButton
Flag the --perm option


mpermButton

javax.swing.JCheckBox mpermButton
Flag the --mperm option


ciButton

javax.swing.JCheckBox ciButton
Flag the ci option


adjustButton

javax.swing.JCheckBox adjustButton
Flag the --adjust button


ciText

javax.swing.JTextField ciText
Allow the user to set the --ci parameter


mpermText

javax.swing.JTextField mpermText
Allow the user to set the --mperm perameter

Class edu.harvard.mgh.purcell.gPLINK2.forms.AlleleFreq extends Form implements Serializable

Serialized Fields

freqButton

javax.swing.JRadioButton freqButton
Buttons that allow the user to select the --freq


countButton

javax.swing.JRadioButton countButton
Buttons that allow the user to select the --count


withinButton

javax.swing.JRadioButton withinButton
Allows the user to specify an optional --within


withinField

javax.swing.JTextField withinField
Picks the --within file


pickWithin

Form.BrowseButton pickWithin
button pick the file associated with --within

Class edu.harvard.mgh.purcell.gPLINK2.forms.Basic extends Form implements Serializable

Class edu.harvard.mgh.purcell.gPLINK2.forms.CCAssoc extends Form implements Serializable

Serialized Fields

ciButton

javax.swing.JCheckBox ciButton

adjustButton

javax.swing.JCheckBox adjustButton

cellButton

javax.swing.JCheckBox cellButton

mperm2Button

javax.swing.JRadioButton mperm2Button

perm2Button

javax.swing.JRadioButton perm2Button

mGenButton

javax.swing.JRadioButton mGenButton

mTrendButton

javax.swing.JRadioButton mTrendButton

mDomButton

javax.swing.JRadioButton mDomButton

mRecButton

javax.swing.JRadioButton mRecButton

mBestButton

javax.swing.JRadioButton mBestButton

ciText

javax.swing.JTextField ciText

cText

javax.swing.JTextField cText

mperm2Text

javax.swing.JTextField mperm2Text

Class edu.harvard.mgh.purcell.gPLINK2.forms.Clustering extends Form implements Serializable

Serialized Fields

ppcButton

javax.swing.JCheckBox ppcButton

ccButton

javax.swing.JCheckBox ccButton

kButton

javax.swing.JCheckBox kButton

ibmButton

javax.swing.JCheckBox ibmButton

matchButton

javax.swing.JCheckBox matchButton

matchTButton

javax.swing.JCheckBox matchTButton

qmatchButton

javax.swing.JCheckBox qmatchButton

mcButton

javax.swing.JCheckBox mcButton

mccButton

javax.swing.JCheckBox mccButton

readGText

javax.swing.JTextField readGText

ppcText

javax.swing.JTextField ppcText

pibsGText

javax.swing.JTextField pibsGText

mcText

javax.swing.JTextField mcText

mcc1Text

javax.swing.JTextField mcc1Text

mcc2Text

javax.swing.JTextField mcc2Text

kText

javax.swing.JTextField kText

ibmText

javax.swing.JTextField ibmText

matchText

javax.swing.JTextField matchText

matchTText

javax.swing.JTextField matchTText

qmatchText

javax.swing.JTextField qmatchText

qtText

javax.swing.JTextField qtText

readGBrowse

Form.BrowseButton readGBrowse

matchBrowse

Form.BrowseButton matchBrowse

matchTBrowse

Form.BrowseButton matchTBrowse

qmatchBrowse

Form.BrowseButton qmatchBrowse

qmatchQTBrowse

Form.BrowseButton qmatchQTBrowse

Class edu.harvard.mgh.purcell.gPLINK2.forms.FamAssoc extends Form implements Serializable

Serialized Fields

tdtButton

javax.swing.JRadioButton tdtButton

pooButton

javax.swing.JRadioButton pooButton

mpermButton

javax.swing.JCheckBox mpermButton

ciButton

javax.swing.JCheckBox ciButton

permButton

javax.swing.JCheckBox permButton

matButton

javax.swing.JCheckBox matButton

patButton

javax.swing.JCheckBox patButton

parent1Button

javax.swing.JCheckBox parent1Button

parent2Button

javax.swing.JCheckBox parent2Button

mpermText

javax.swing.JTextField mpermText

ciText

javax.swing.JTextField ciText

Class edu.harvard.mgh.purcell.gPLINK2.forms.GenFileSet extends Form implements Serializable

Serialized Fields

recode

javax.swing.JRadioButton recode

recodeAD

javax.swing.JRadioButton recodeAD

recode12

javax.swing.JRadioButton recode12

recodeHV

javax.swing.JRadioButton recodeHV

makeBin

javax.swing.JRadioButton makeBin

Class edu.harvard.mgh.purcell.gPLINK2.forms.HapCCAssoc extends Form implements Serializable

Serialized Fields

hapListButton

javax.swing.JRadioButton hapListButton

hapWindowButton

javax.swing.JRadioButton hapWindowButton

hapListText

javax.swing.JTextField hapListText

hapWindowText

javax.swing.JTextField hapWindowText

hapListBrowse

Form.BrowseButton hapListBrowse

Class edu.harvard.mgh.purcell.gPLINK2.forms.HaploFreq extends Form implements Serializable

Serialized Fields

hapListBrowse

Form.BrowseButton hapListBrowse

hapListButton

javax.swing.JRadioButton hapListButton

hapWindowButton

javax.swing.JRadioButton hapWindowButton

hapListText

javax.swing.JTextField hapListText

hapWindowText

javax.swing.JTextField hapWindowText

Class edu.harvard.mgh.purcell.gPLINK2.forms.HaploPhase extends Form implements Serializable

Serialized Fields

hapListBrowse

Form.BrowseButton hapListBrowse

hapListButton

javax.swing.JRadioButton hapListButton

hapWindowButton

javax.swing.JRadioButton hapWindowButton

hapListText

javax.swing.JTextField hapListText

hapWindowText

javax.swing.JTextField hapWindowText

Class edu.harvard.mgh.purcell.gPLINK2.forms.HapTDTAssoc extends Form implements Serializable

Serialized Fields

hapListButton

javax.swing.JRadioButton hapListButton

hapWindowButton

javax.swing.JRadioButton hapWindowButton

hapListText

javax.swing.JTextField hapListText

hapWindowText

javax.swing.JTextField hapWindowText

hapListBrowse

Form.BrowseButton hapListBrowse

Class edu.harvard.mgh.purcell.gPLINK2.forms.HardyWinEq extends Form implements Serializable

Class edu.harvard.mgh.purcell.gPLINK2.forms.HomozRuns extends Form implements Serializable

Serialized Fields

homSNPButton

javax.swing.JRadioButton homSNPButton

homKBButton

javax.swing.JRadioButton homKBButton

homGroupButton

javax.swing.JCheckBox homGroupButton

homMatchButton

javax.swing.JCheckBox homMatchButton

homHetButton

javax.swing.JCheckBox homHetButton

homVerboseButton

javax.swing.JCheckBox homVerboseButton

homSNPText

javax.swing.JTextField homSNPText

homKBText

javax.swing.JTextField homKBText

homMatchText

javax.swing.JTextField homMatchText

homHetText

javax.swing.JTextField homHetText

Class edu.harvard.mgh.purcell.gPLINK2.forms.IBSdist extends Form implements Serializable

Serialized Fields

ibsDistButton

javax.swing.JCheckBox ibsDistButton
flag the creation of a ibs distatnce matrix

Class edu.harvard.mgh.purcell.gPLINK2.forms.IndHetz extends Form implements Serializable

Class edu.harvard.mgh.purcell.gPLINK2.forms.MendelErr extends Form implements Serializable

Class edu.harvard.mgh.purcell.gPLINK2.forms.Merge extends Form implements Serializable

Serialized Fields

targetText

Merge.TextSelectPanel targetText

targetBin

Merge.BinSelectPanel targetBin

targetTXT

Merge.ListSelectPanel targetTXT

mergeInputs

javax.swing.JTabbedPane mergeInputs

recode

javax.swing.JRadioButton recode

recodeAD

javax.swing.JRadioButton recodeAD

recode12

javax.swing.JRadioButton recode12

recodeHV

javax.swing.JRadioButton recodeHV

makeBin

javax.swing.JRadioButton makeBin

recodeOp

javax.swing.JPanel recodeOp

op1

javax.swing.JRadioButton op1

op2

javax.swing.JRadioButton op2

op3

javax.swing.JRadioButton op3

op4

javax.swing.JRadioButton op4

op5

javax.swing.JRadioButton op5

op6

javax.swing.JRadioButton op6

op7

javax.swing.JRadioButton op7

optional

javax.swing.JPanel optional

Class edu.harvard.mgh.purcell.gPLINK2.forms.Missing extends Form implements Serializable

Serialized Fields

rates

javax.swing.JRadioButton rates
A JRadioButton to flag the "--missing" option


testByPheno

javax.swing.JRadioButton testByPheno
A JRadioButton to flag the "--test-missing" option that looks for missing phenotype


testByGeno

javax.swing.JRadioButton testByGeno
A JRadioButton to flag (--test-mishap) with optional (--mishap-window)


mishapNum

javax.swing.JTextField mishapNum
A JTextField holding the --mishap-window arguemnt.

Class edu.harvard.mgh.purcell.gPLINK2.forms.NearNeigh extends Form implements Serializable

Serialized Fields

neigh1Text

javax.swing.JTextField neigh1Text

neigh2Text

javax.swing.JTextField neigh2Text

genomicText

javax.swing.JTextField genomicText

neighButton

javax.swing.JCheckBox neighButton

Class edu.harvard.mgh.purcell.gPLINK2.forms.QuantTrtInt extends Form implements Serializable

Serialized Fields

coverFile

javax.swing.JTextField coverFile
The covarienance file associated with this test

Class edu.harvard.mgh.purcell.gPLINK2.forms.Regression extends Form implements Serializable

Serialized Fields

freqButton

javax.swing.JRadioButton freqButton

genoButton

javax.swing.JRadioButton genoButton

covarButton

javax.swing.JCheckBox covarButton

covarField

javax.swing.JTextField covarField

pickCovar

Form.BrowseButton pickCovar

Class edu.harvard.mgh.purcell.gPLINK2.forms.SetAssoc extends Form implements Serializable

Serialized Fields

t2Button

javax.swing.JRadioButton t2Button

setButton

javax.swing.JRadioButton setButton

mpButton

javax.swing.JCheckBox mpButton

setMinButton

javax.swing.JCheckBox setMinButton

setMaxButton

javax.swing.JCheckBox setMaxButton

setText

javax.swing.JTextField setText

mpText

javax.swing.JTextField mpText

setMinText

javax.swing.JTextField setMinText

setMaxText

javax.swing.JTextField setMaxText

setBrowse

Form.BrowseButton setBrowse

Class edu.harvard.mgh.purcell.gPLINK2.forms.StratAnaly extends Form implements Serializable

Serialized Fields

mhButton

javax.swing.JRadioButton mhButton

mh2Button

javax.swing.JRadioButton mh2Button

homogButton

javax.swing.JRadioButton homogButton

withinButton

javax.swing.JRadioButton withinButton

familyButton

javax.swing.JRadioButton familyButton

ciButton

javax.swing.JCheckBox ciButton

bdButton

javax.swing.JCheckBox bdButton

adjustButton

javax.swing.JCheckBox adjustButton

withinText

javax.swing.JTextField withinText

ciText

javax.swing.JTextField ciText

withinBrowse

Form.BrowseButton withinBrowse

Class edu.harvard.mgh.purcell.gPLINK2.forms.Validate extends Form implements Serializable