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rates
- Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
Missing
A JRadioButton to flag the "--missing" option
readGBrowse
- Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
Clustering
readGText
- Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
Clustering
readLock()
- Method in class edu.harvard.mgh.purcell.gCLINE.data.
Lock
Read the lock code from the file.
readLogs
- Variable in class edu.harvard.mgh.purcell.gCLINE.data.
AutoUpdater
This runs every 5 seconds ideal but can be delayed if there isn't enough processor space.
recode
- Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
GenFileSet
recode
- Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
Merge
recode12
- Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
GenFileSet
recode12
- Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
Merge
recodeAD
- Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
GenFileSet
recodeAD
- Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
Merge
recodeHV
- Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
GenFileSet
recodeHV
- Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
Merge
recodeOp
- Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
Merge
Record
- Class in
edu.harvard.mgh.purcell.gCLINE.data
This class manages the operation annotations.
Record()
- Constructor for class edu.harvard.mgh.purcell.gCLINE.data.
Record
Create a Record with null or empty fields.
Record(StartFrame)
- Constructor for class edu.harvard.mgh.purcell.gCLINE.data.
Record
Create a Record initalized to a particular StartFrame.
Record(StartFrame, String)
- Constructor for class edu.harvard.mgh.purcell.gCLINE.data.
Record
Create a Record.
Record(StartFrame, String, String, String, String, String, SshClient)
- Constructor for class edu.harvard.mgh.purcell.gCLINE.data.
Record
Create a Record.
Record.myHostKeyValidator
- Class in
edu.harvard.mgh.purcell.gCLINE.data
This is a host key validator that automatically accepts any host key sent but doesn't actually save any of them.
Record.myHostKeyValidator()
- Constructor for class edu.harvard.mgh.purcell.gCLINE.data.
Record.myHostKeyValidator
Regression
- Class in
edu.harvard.mgh.purcell.gPLINK2.forms
A linear/logistic regression form.
Regression(GPLINK)
- Constructor for class edu.harvard.mgh.purcell.gPLINK2.forms.
Regression
REMOTE_CONFIG_FILE
- Static variable in interface edu.harvard.mgh.purcell.gCLINE.data.
KeyWords
file that holds the remote configuration
REMOTE_FOLDER_KEY
- Static variable in interface edu.harvard.mgh.purcell.gCLINE.data.
KeyWords
the remote project folder name
REMOTE_GLOBAL_CONFIG
- Static variable in interface edu.harvard.mgh.purcell.gCLINE.data.
KeyWords
REMOTE_UPDATE_INTERVAL_KEY
- Static variable in interface edu.harvard.mgh.purcell.gCLINE.data.
KeyWords
remote update interval key
remoteBrowse
- Variable in class edu.harvard.mgh.purcell.gPLINK2.
PLINK_Open
remoteChooser
- Variable in class edu.harvard.mgh.purcell.gCLINE.tester.
Open
Our file choosing class for the remote directory.
remoteChooser
- Variable in class edu.harvard.mgh.purcell.gPLINK2.
PLINK_Open
Our file choosing class for the remote directory.
remoteConfig
- Variable in class edu.harvard.mgh.purcell.gCLINE.data.
Record
remoteConfig is a Properties that holds the information for the remote connection.
remoteFile
- Variable in class edu.harvard.mgh.purcell.gCLINE.data.
Lock
The directory that the remote lock file is in
remoteFile(String)
- Method in class edu.harvard.mgh.purcell.gCLINE.data.
OperationInfo
remoteFilenames
- Variable in class edu.harvard.mgh.purcell.gCLINE.
PopUpMenu
An array of the full file names of selected remote files
remoteFiles
- Variable in class edu.harvard.mgh.purcell.gCLINE.
TransfureFiles
remoteFlag
- Variable in class edu.harvard.mgh.purcell.gCLINE.tester.
Open
Let the user flag this project as remote.
remoteFlag
- Variable in class edu.harvard.mgh.purcell.gPLINK2.
PLINK_Open
Let the user flag this project as remote.
remoteFolder
- Variable in class edu.harvard.mgh.purcell.gCLINE.
TransfureFiles
remotePanel
- Variable in class edu.harvard.mgh.purcell.gCLINE.tester.
Open
A panel containing all the fields pertinate to the remote directory.
remotePanel
- Variable in class edu.harvard.mgh.purcell.gPLINK2.
PLINK_Open
A panel containing all the fields pertinate to the remote directory.
remotePicker
- Variable in class edu.harvard.mgh.purcell.gCLINE.general.
GCFileChooser
A dialog that alows the user to select a remote file.
remotePicks
- Variable in class edu.harvard.mgh.purcell.gCLINE.general.
GCFileChooser
remoteProject
- Variable in class edu.harvard.mgh.purcell.gCLINE.tester.
Open
Let the user look at the remote project directory
remoteProject
- Variable in class edu.harvard.mgh.purcell.gPLINK2.
PLINK_Open
Let the user look at the remote project directory
removeFileChoosenListener(GCFileChooser.FileChoosenListener)
- Method in class edu.harvard.mgh.purcell.gCLINE.general.
GCFileChooser
Remove a listener from the list.
removeFileFromOp
- Variable in class edu.harvard.mgh.purcell.gCLINE.
PopUpMenu
removeOperation(String)
- Method in class edu.harvard.mgh.purcell.gCLINE.data.
Record
Remove an operation from the document.
replaceOp
- Variable in class edu.harvard.mgh.purcell.gCLINE.
EditOpDialog
reset
- Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.
ThresholdDialog
Reset all the defaults
resetButton
- Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.
ThresholdDialog
Buttons to operate this dialog
resetFilter()
- Method in class edu.harvard.mgh.purcell.gPLINK2.baseForm.
Form
resetThreshold()
- Method in class edu.harvard.mgh.purcell.gPLINK2.baseForm.
Form
restore
- Variable in class edu.harvard.mgh.purcell.gPLINK2.
PlinkMenuBar
RestoreDataDialog
- Class in
edu.harvard.mgh.purcell.gCLINE
RestoreDataDialog(JFrame, Record)
- Constructor for class edu.harvard.mgh.purcell.gCLINE.
RestoreDataDialog
root
- Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.
OutputPane
The proposed output root.
rootFrame
- Variable in class edu.harvard.mgh.purcell.gCLINE.general.
ErrorManager
The JFrame the messages are attaced to.
rootList
- Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.
OutputPane
A Vector of Strings that are the files in the home directory that end with the operation log extention.
run()
- Method in class edu.harvard.mgh.purcell.gCLINE.data.
RunCommand
run()
- Method in class edu.harvard.mgh.purcell.gCLINE.pane.
FolderView.UpdateJList
run()
- Method in class edu.harvard.mgh.purcell.gCLINE.
StartFrame.Download
Notify the GUI that we are transfuring files and then run transfure the files.
run()
- Method in class edu.harvard.mgh.purcell.gCLINE.
StartFrame.Upload
run()
- Method in class edu.harvard.mgh.purcell.gCLINE.
TransfureFiles
RunCommand
- Class in
edu.harvard.mgh.purcell.gCLINE.data
RunCommand(String, Record)
- Constructor for class edu.harvard.mgh.purcell.gCLINE.data.
RunCommand
RunCommand(String, Record, boolean)
- Constructor for class edu.harvard.mgh.purcell.gCLINE.data.
RunCommand
RunCommand(String, SshClient)
- Constructor for class edu.harvard.mgh.purcell.gCLINE.data.
RunCommand
RUNNING
- Static variable in class edu.harvard.mgh.purcell.gCLINE.data.
AutoUpdater
Flags a running operation
runningIcon
- Variable in class edu.harvard.mgh.purcell.gCLINE.data.
AutoUpdater.MyRenderer
Overview
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