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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[], 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.
Overview
Package
Class
Use
Tree
Deprecated
Index
Help
PREV LETTER
NEXT LETTER
FRAMES
NO FRAMES
All Classes
A
B
C
D
E
F
G
H
I
K
L
M
N
O
P
Q
R
S
T
U
V
W