A B C D E F G H I K L M N O P Q R S T U V W

P

P1_KEY - Static variable in interface edu.harvard.mgh.purcell.gCLINE.data.KeyWords
key for the project that was opened latest
P2_KEY - Static variable in interface edu.harvard.mgh.purcell.gCLINE.data.KeyWords
key for the second project
P3_KEY - Static variable in interface edu.harvard.mgh.purcell.gCLINE.data.KeyWords
key for the third project
P4_KEY - Static variable in interface edu.harvard.mgh.purcell.gCLINE.data.KeyWords
key for the forth project
parent - Variable in class edu.harvard.mgh.purcell.gCLINE.general.GCFileChooser
Attached the dialogs to our main window and access the record through
parent - Variable in class edu.harvard.mgh.purcell.gCLINE.tester.MenuBarMain
 
parent - Variable in class edu.harvard.mgh.purcell.gCLINE.tester.Open
The main frame of the program.
parent - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.FilterDialog
 
parent - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.Form
The GPLINK instance that this form is attached to.
parent - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.InputPane
The GPLINK istance this is attached to.
parent - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.ThresholdDialog
The form that this dialog is attached to
parent - Variable in class edu.harvard.mgh.purcell.gPLINK2.PLINK_Open
The JFrame of the program.
parent1Button - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.FamAssoc
 
parent2 - Variable in class edu.harvard.mgh.purcell.gCLINE.general.GCFileChooser
 
parent2Button - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.FamAssoc
 
parentFile(String[], DefaultMutableTreeNode) - Method in class edu.harvard.mgh.purcell.gCLINE.HierarchyDialog
 
parentForm - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.InputPane
The dialog that we want to attach our file name browsing window to.
parentForm - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.OutputPane
The form this output pane is going to appear in.
parentOp(String, DefaultMutableTreeNode) - Method in class edu.harvard.mgh.purcell.gCLINE.HierarchyDialog
 
patButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.FamAssoc
 
PCC_DEFAULT - Static variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Clustering
 
pedBrowse - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.InputPane
A BrowseButton that selects the ped file.
pedBrowse - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Merge.TextSelectPanel
 
pedButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.OpenHapDialog
A JButton that triggers the ped file browse.
pedField - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.InputPane
A JTextField that holds the ped file name
pedField - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Merge.TextSelectPanel
 
pedFile - Variable in class edu.harvard.mgh.purcell.gPLINK2.OpenHapDialog
A JTextField that holds the full ped file path.
pedInfoRB - Variable in class edu.harvard.mgh.purcell.gPLINK2.OpenHapDialog
A JRadioButton to flag the ped/info file option for haploview
pedSuffex - Static variable in class edu.harvard.mgh.purcell.gPLINK2.OpenHapDialog
A String array that holds all the suffix's that flag a ped file.
perm2Button - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.CCAssoc
 
permButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.AlleleAssoc
Flag the --perm option
permButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.FamAssoc
 
PIBS_G_DEFAULT - Static variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Clustering
 
pibsGText - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Clustering
 
pick - Variable in class edu.harvard.mgh.purcell.gCLINE.LinkNewFileDialog.BrowseButton
 
pick - Variable in class edu.harvard.mgh.purcell.gPLINK2.AddGenericOp.BrowseButton
 
pick - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.FilterDialog.BrowseButton
 
pick - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.Form.BrowseButton
 
pick - Variable in class edu.harvard.mgh.purcell.gPLINK2.PLINK_Config.BrowseButton
A GCFileChooser we use to pick the file.
pickCovar - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Regression
 
pickFilter - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.FilterDialog
 
pickList - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.FilterDialog
 
pickMap - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.FilterDialog
 
pickWithin - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.AlleleFreq
button pick the file associated with --within
plink - Variable in class edu.harvard.mgh.purcell.gPLINK2.PlinkMenuBar
 
PLINK_Config - Class in edu.harvard.mgh.purcell.gPLINK2
A Configure dialog that is specific to PLINK.
PLINK_Config(GPLINK) - Constructor for class edu.harvard.mgh.purcell.gPLINK2.PLINK_Config
Create an instance of the configuration dialog.
PLINK_Config.BrowseButton - Class in edu.harvard.mgh.purcell.gPLINK2
A subclass that creates a browse button that passes the file name to a target JTextField.
PLINK_Config.BrowseButton(JTextField) - Constructor for class edu.harvard.mgh.purcell.gPLINK2.PLINK_Config.BrowseButton
Create a browse button.
PLINK_Config.BrowseButton(JTextField, boolean) - Constructor for class edu.harvard.mgh.purcell.gPLINK2.PLINK_Config.BrowseButton
 
PLINK_Execute - Class in edu.harvard.mgh.purcell.gPLINK2
Create a dialog that will pass the plink command to either a local or remote computer depending on weather the project is flagged as remote or local.
PLINK_Execute(GPLINK, String) - Constructor for class edu.harvard.mgh.purcell.gPLINK2.PLINK_Execute
Create an instance of this dialog.
PLINK_Import - Class in edu.harvard.mgh.purcell.gPLINK2
An extention of JDialog that imports a new command into OpView from a log file.
PLINK_Import(StartFrame, Project) - Constructor for class edu.harvard.mgh.purcell.gPLINK2.PLINK_Import
Create a JDialog that will allow the user to input plink operations from log files in their home directory.
PLINK_Import.ExitStatus - Enum in edu.harvard.mgh.purcell.gPLINK2
A boolean flag that is true if the operation is done and false otherwise.
PLINK_Import.ExitStatus() - Constructor for enum edu.harvard.mgh.purcell.gPLINK2.PLINK_Import.ExitStatus
 
PLINK_Open - Class in edu.harvard.mgh.purcell.gPLINK2
Create a Dialog to open a new PLINK project.
PLINK_Open(GPLINK) - Constructor for class edu.harvard.mgh.purcell.gPLINK2.PLINK_Open
Create a dialog that will open up a new project and establish an ssh connection.
PLINK_Open(GPLINK, String) - Constructor for class edu.harvard.mgh.purcell.gPLINK2.PLINK_Open
Create a dialog that will open a new Project.
PLINK_Open(GPLINK, String, String, String, String, String) - Constructor for class edu.harvard.mgh.purcell.gPLINK2.PLINK_Open
Create a dialog that will open a new Project.
PLINK_Open.gCLINEFilter - Class in edu.harvard.mgh.purcell.gPLINK2
A FileFilter that will look for directories
PLINK_Open.gCLINEFilter() - Constructor for class edu.harvard.mgh.purcell.gPLINK2.PLINK_Open.gCLINEFilter
 
PLINK_PATH - Static variable in class edu.harvard.mgh.purcell.gPLINK2.data.Project
 
PLINK_PREFIX - Static variable in class edu.harvard.mgh.purcell.gPLINK2.data.Project
 
PlinkMenuBar - Class in edu.harvard.mgh.purcell.gPLINK2
A Menu Bar that is specific to PLINK.
PlinkMenuBar(GPLINK) - Constructor for class edu.harvard.mgh.purcell.gPLINK2.PlinkMenuBar
Create an instance of this plink specific menu bar.
plinkPath - Variable in class edu.harvard.mgh.purcell.gPLINK2.PLINK_Config
A JTextField for the plink path.
plinkPrefix - Variable in class edu.harvard.mgh.purcell.gPLINK2.PLINK_Config
A JTextField for the plink prefix command.
pooButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.FamAssoc
 
populateFields(String, String) - Method in class edu.harvard.mgh.purcell.gPLINK2.OpenHapDialog
Populate the fields based on the file and operation name.
populateNodes(Document) - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
Populate the operations and global file notes from a Document.
PopUpMenu - Class in edu.harvard.mgh.purcell.gCLINE
An abstract class that lays out the general popup menu that appears in both the operations and folder viewers.
PopUpMenu(StartFrame, Record, String[], String[]) - Constructor for class edu.harvard.mgh.purcell.gCLINE.PopUpMenu
 
port - Variable in class edu.harvard.mgh.purcell.gCLINE.tester.Open
 
port - Variable in class edu.harvard.mgh.purcell.gPLINK2.PLINK_Open
A JTextField that keeps the port number as a string.
PORT_KEY - Static variable in interface edu.harvard.mgh.purcell.gCLINE.data.KeyWords
A string that states the remote port key.
ppcButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Clustering
 
ppcText - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Clustering
 
printfull() - Method in class edu.harvard.mgh.purcell.gCLINE.data.OperationInfo
Print out the operation to a string.
process() - Method in class edu.harvard.mgh.purcell.gCLINE.general.Configure
Set all the configurations in the project and save these configurations.
process - Variable in class edu.harvard.mgh.purcell.gCLINE.LinkNewFileDialog
The ActionListener that adds the file to the operation.
process() - Method in class edu.harvard.mgh.purcell.gCLINE.tester.TestFrame.StartFrameConfig
 
process - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.FilterDialog
 
process() - Method in class edu.harvard.mgh.purcell.gPLINK2.baseForm.Form
Process forms in general.
process() - Method in class edu.harvard.mgh.purcell.gPLINK2.baseForm.InputPane
Based on the fields in the input pane generate the input section of the PLINK command line.
process() - Method in class edu.harvard.mgh.purcell.gPLINK2.baseForm.OutputPane
 
process - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.ThresholdDialog
Process the dialog to command line.
process() - Method in class edu.harvard.mgh.purcell.gPLINK2.PLINK_Config
Set the fields in the project to reflect their corrisponding fields in this dialog.
process() - Method in class edu.harvard.mgh.purcell.gPLINK2.PLINK_Import
Take the options selected on the form and add an appropreate operation.
processBody() - Method in class edu.harvard.mgh.purcell.gPLINK2.baseForm.Form
Create the commandline based on the fields of this form.
processBody() - Method in class edu.harvard.mgh.purcell.gPLINK2.forms.AlleleAssoc
Pull the commandline from this form
processBody() - Method in class edu.harvard.mgh.purcell.gPLINK2.forms.AlleleFreq
Pull the command line from the form.
processBody() - Method in class edu.harvard.mgh.purcell.gPLINK2.forms.Basic
 
processBody() - Method in class edu.harvard.mgh.purcell.gPLINK2.forms.CCAssoc
 
processBody() - Method in class edu.harvard.mgh.purcell.gPLINK2.forms.Clustering
process the body of the form to generate the plink command
processBody() - Method in class edu.harvard.mgh.purcell.gPLINK2.forms.FamAssoc
 
processBody() - Method in class edu.harvard.mgh.purcell.gPLINK2.forms.GenFileSet
 
processBody() - Method in class edu.harvard.mgh.purcell.gPLINK2.forms.HapCCAssoc
 
processBody() - Method in class edu.harvard.mgh.purcell.gPLINK2.forms.HaploFreq
 
processBody() - Method in class edu.harvard.mgh.purcell.gPLINK2.forms.HaploPhase
 
processBody() - Method in class edu.harvard.mgh.purcell.gPLINK2.forms.HapTDTAssoc
 
processBody() - Method in class edu.harvard.mgh.purcell.gPLINK2.forms.HardyWinEq
 
processBody() - Method in class edu.harvard.mgh.purcell.gPLINK2.forms.HomozRuns
 
processBody() - Method in class edu.harvard.mgh.purcell.gPLINK2.forms.IBSdist
 
processBody() - Method in class edu.harvard.mgh.purcell.gPLINK2.forms.IndHetz
 
processBody() - Method in class edu.harvard.mgh.purcell.gPLINK2.forms.MendelErr
 
processBody() - Method in class edu.harvard.mgh.purcell.gPLINK2.forms.Merge
 
processBody() - Method in class edu.harvard.mgh.purcell.gPLINK2.forms.Missing
 
processBody() - Method in class edu.harvard.mgh.purcell.gPLINK2.forms.NearNeigh
 
processBody() - Method in class edu.harvard.mgh.purcell.gPLINK2.forms.QuantTrtInt
 
processBody() - Method in class edu.harvard.mgh.purcell.gPLINK2.forms.Regression
 
processBody() - Method in class edu.harvard.mgh.purcell.gPLINK2.forms.SetAssoc
 
processBody() - Method in class edu.harvard.mgh.purcell.gPLINK2.forms.StratAnaly
 
processBody() - Method in class edu.harvard.mgh.purcell.gPLINK2.forms.Validate
 
processIn - Variable in class edu.harvard.mgh.purcell.gPLINK2.AddGenericOp
Listen to the temperary JTextField for input file to add to the operation.
processNodes() - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
Create a Document from the operations and global file notes that we can then write as an xml document easily.
processOpName(String) - Method in class edu.harvard.mgh.purcell.gCLINE.data.AutoUpdater
Pull the operation name from the text in the operation node.
processOut - Variable in class edu.harvard.mgh.purcell.gPLINK2.AddGenericOp
Listen to the temperary JTextField for the output file to add to the operation
Project - Class in edu.harvard.mgh.purcell.gPLINK2.data
 
Project() - Constructor for class edu.harvard.mgh.purcell.gPLINK2.data.Project
 
Project(GPLINK) - Constructor for class edu.harvard.mgh.purcell.gPLINK2.data.Project
 
Project(GPLINK, String) - Constructor for class edu.harvard.mgh.purcell.gPLINK2.data.Project
 
Project(GPLINK, String, String, String, String, String, SshClient) - Constructor for class edu.harvard.mgh.purcell.gPLINK2.data.Project
 
project1 - Variable in class edu.harvard.mgh.purcell.gCLINE.tester.MenuBarMain
 
project1 - Variable in class edu.harvard.mgh.purcell.gPLINK2.PlinkMenuBar
A String holding the most recent project that have been opened.
project2 - Variable in class edu.harvard.mgh.purcell.gCLINE.tester.MenuBarMain
 
project2 - Variable in class edu.harvard.mgh.purcell.gPLINK2.PlinkMenuBar
A String holding the second most recent project that have been opened.
project3 - Variable in class edu.harvard.mgh.purcell.gCLINE.tester.MenuBarMain
 
project3 - Variable in class edu.harvard.mgh.purcell.gPLINK2.PlinkMenuBar
A String holding the third most recent project that have been opened.
project4 - Variable in class edu.harvard.mgh.purcell.gCLINE.tester.MenuBarMain
 
project4 - Variable in class edu.harvard.mgh.purcell.gPLINK2.PlinkMenuBar
A String holding the forth most recent project that have been opened.
properClosing() - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
Close the Record up properly.
properClosing - Variable in class edu.harvard.mgh.purcell.gCLINE.StartFrame
A WindowListener that closes the gui properly.
properClosing - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.FilterDialog
 
properClosing - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.ThresholdDialog
 
properClosing - Variable in class edu.harvard.mgh.purcell.gPLINK2.GPLINK
Create a windowListener that will properly close this class.

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