Serialized Form
Package com.sshtools.common.authentication |
jListAuths
javax.swing.JList jListAuths
messageLabel
javax.swing.JLabel messageLabel
cancelled
boolean cancelled
text
javax.swing.JTextArea text
cancelled
boolean cancelled
instructionLabel
javax.swing.JLabel instructionLabel
buttonsPanel
javax.swing.JPanel buttonsPanel
promptReply
javax.swing.text.JTextComponent[] promptReply
jButtonCancel
javax.swing.JButton jButtonCancel
jButtonOK
javax.swing.JButton jButtonOK
message
javax.swing.JLabel message
jPasswordField
javax.swing.JPasswordField jPasswordField
userCancelled
boolean userCancelled
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 |
Package com.sshtools.common.configuration |
Package com.sshtools.common.keygen |
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
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
close
javax.swing.JButton close
generate
javax.swing.JButton generate
keygen
KeygenPanel keygen
Package com.sshtools.common.mru |
currentElement
java.lang.String currentElement
mru
MRUList mru
model
MRUListModel model
Package com.sshtools.common.ui |
application
SshToolsApplication application
parent
java.awt.Component parent
trueIcon
javax.swing.Icon trueIcon
falseIcon
javax.swing.Icon falseIcon
application
SshToolsApplication application
container
SshToolsApplicationContainer container
textLabel
javax.swing.JLabel textLabel
iconLabel
javax.swing.JLabel iconLabel
action
javax.swing.Action action
lafChooser
javax.swing.JComboBox lafChooser
hosts
javax.swing.JList hosts
hostKeyVerifier
AbstractKnownHostsKeyVerification hostKeyVerifier
remove
javax.swing.JButton remove
model
HostsTab.HostsListModel model
icon
ResourceIcon icon
alignBottomRight
boolean alignBottomRight
constraints
java.awt.GridBagConstraints constraints
text
java.lang.String text
log
org.apache.commons.logging.Log log
application
SshToolsApplication application
positiveBackground
java.awt.Color positiveBackground
symbols
java.text.DecimalFormatSymbols symbols
numberFormat
java.text.NumberFormat numberFormat
selectAllOnFocusGain
boolean selectAllOnFocusGain
wColumnWidth
int wColumnWidth
selectedOption
Option selectedOption
callback
OptionCallback callback
defaultButton
javax.swing.JButton defaultButton
log
org.apache.commons.logging.Log log
tabber
Tabber tabber
cancelled
boolean cancelled
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
cls
java.lang.Class<T> cls
provider
SessionProvider provider
panel
SshToolsApplicationSessionPanel panel
provider
SessionProvider provider
profile
SshToolsConnectionProfile profile
ssh
SshClient ssh
disconnectOnClose
boolean disconnectOnClose
panel
SshToolsApplicationSessionPanel panel
provider
SessionProvider provider
profile
SshToolsConnectionProfile profile
ssh
SshClient ssh
disconnectOnClose
boolean disconnectOnClose
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
panel
SshToolsApplicationPanel panel
application
SshToolsApplication application
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
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
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
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
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
log
org.apache.commons.logging.Log log
currentConnectionProfile
SshToolsConnectionProfile currentConnectionProfile
manager
SessionManager manager
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
log
org.apache.commons.logging.Log log
tabber
Tabber tabber
profile
SshToolsConnectionProfile profile
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
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
listeners
javax.swing.event.EventListenerList listeners
startedIcon
javax.swing.Icon startedIcon
stoppedIcon
javax.swing.Icon stoppedIcon
failedIcon
javax.swing.Icon failedIcon
errorMsg
java.lang.String errorMsg
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
text
java.lang.String text
hideText
boolean hideText
hideText
boolean hideText
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 |
Package com.sshtools.daemon.platform |
Package com.sshtools.daemon.terminal |
Package com.sshtools.daemon.util |
ignoreCase
boolean ignoreCase
pattern
java.lang.String pattern
digitWildcard
java.lang.Character digitWildcard
Package com.sshtools.j2ssh |
Package com.sshtools.j2ssh.agent |
Package com.sshtools.j2ssh.authentication |
state
int state
Package com.sshtools.j2ssh.configuration |
Package com.sshtools.j2ssh.connection |
Package com.sshtools.j2ssh.forwarding |
Package com.sshtools.j2ssh.io |
serialVersionUID: 200L
value
java.lang.Long value
serialVersionUID: 200L
bigInt
java.math.BigInteger bigInt
Package com.sshtools.j2ssh.transport |
lastError
java.io.IOException lastError
reason
java.lang.String reason
Package com.sshtools.j2ssh.transport.kex |
Package com.sshtools.j2ssh.transport.publickey |
Package com.sshtools.j2ssh.util |
state
int state
Package edu.harvard.mgh.purcell.gCLINE |
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.
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
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
ancesters
javax.swing.JTree ancesters
decendents
javax.swing.JTree decendents
data
Record data
opName
java.lang.String opName
fileName
java.lang.String fileName
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.
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
logger
org.apache.log4j.Logger logger
- A logger for this class
fileField
javax.swing.JTextField fileField
localChooser
GCFileChooser localChooser
data
Record data
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 |
sucessIcon
javax.swing.Icon sucessIcon
failIcon
javax.swing.Icon failIcon
runningIcon
javax.swing.Icon runningIcon
fileInfoIcon
javax.swing.Icon fileInfoIcon
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.
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
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 |
data
Record data
- Access
localChooser
GCFileChooser localChooser
editor
javax.swing.JTextField editor
updateField
javax.swing.JTextField updateField
Package edu.harvard.mgh.purcell.gCLINE.pane |
textdisplay
javax.swing.JTextArea textdisplay
currentFile
javax.swing.JLabel currentFile
Package edu.harvard.mgh.purcell.gCLINE.tester |
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
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.
data
TestFrame.myProject data
Package edu.harvard.mgh.purcell.gPLINK2 |
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
target
javax.swing.JTextField target
pick
GCFileChooser pick
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.
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.
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
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.
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
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.
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 |
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
suffex
java.lang.String suffex
suffexDisc
java.lang.String suffexDisc
target
javax.swing.JTextField target
pick
GCFileChooser pick
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
suffex
java.lang.String suffex
suffexDisc
java.lang.String suffexDisc
target
javax.swing.JTextField target
pick
GCFileChooser pick
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
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.
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 |
Package edu.harvard.mgh.purcell.gPLINK2.forms |
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
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
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
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
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
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
hapListButton
javax.swing.JRadioButton hapListButton
hapWindowButton
javax.swing.JRadioButton hapWindowButton
hapListText
javax.swing.JTextField hapListText
hapWindowText
javax.swing.JTextField hapWindowText
hapListBrowse
Form.BrowseButton hapListBrowse
hapListBrowse
Form.BrowseButton hapListBrowse
hapListButton
javax.swing.JRadioButton hapListButton
hapWindowButton
javax.swing.JRadioButton hapWindowButton
hapListText
javax.swing.JTextField hapListText
hapWindowText
javax.swing.JTextField hapWindowText
hapListBrowse
Form.BrowseButton hapListBrowse
hapListButton
javax.swing.JRadioButton hapListButton
hapWindowButton
javax.swing.JRadioButton hapWindowButton
hapListText
javax.swing.JTextField hapListText
hapWindowText
javax.swing.JTextField hapWindowText
hapListButton
javax.swing.JRadioButton hapListButton
hapWindowButton
javax.swing.JRadioButton hapWindowButton
hapListText
javax.swing.JTextField hapListText
hapWindowText
javax.swing.JTextField hapWindowText
hapListBrowse
Form.BrowseButton hapListBrowse
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
ibsDistButton
javax.swing.JCheckBox ibsDistButton
- flag the creation of a ibs distatnce matrix
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
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.
neigh1Text
javax.swing.JTextField neigh1Text
neigh2Text
javax.swing.JTextField neigh2Text
genomicText
javax.swing.JTextField genomicText
neighButton
javax.swing.JCheckBox neighButton
coverFile
javax.swing.JTextField coverFile
- The covarienance file associated with this test
freqButton
javax.swing.JRadioButton freqButton
genoButton
javax.swing.JRadioButton genoButton
covarButton
javax.swing.JCheckBox covarButton
covarField
javax.swing.JTextField covarField
pickCovar
Form.BrowseButton pickCovar
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
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