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R

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
 

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