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C
cancel()
- Method in class edu.harvard.mgh.purcell.gCLINE.data.
AutoUpdater
runs the Timer's cancel and set the opStatis to null for garbage collection.
cancel
- Variable in class edu.harvard.mgh.purcell.gCLINE.
EditFolderDialog
cancel
- Variable in class edu.harvard.mgh.purcell.gCLINE.
EditOpDialog
cancel
- Variable in class edu.harvard.mgh.purcell.gCLINE.
LinkNewFileDialog
An ActionListener that closes the dialog without doing anything.
cancel
- Variable in class edu.harvard.mgh.purcell.gPLINK2.
AddGenericOp
A JButton that signals the cancelation of the form.
cancel
- Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.
FilterDialog
cancel
- Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.
Form
cancel
- Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.
ThresholdDialog
Cancel the dailog and throw it away without changing things
cancel
- Variable in class edu.harvard.mgh.purcell.gPLINK2.
OpenHapDialog
A JButton to close the dialog without doing anything.
cancelButton
- Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.
FilterDialog
cancelButton
- Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.
ThresholdDialog
Buttons to operate this dialog
CCAssoc
- Class in
edu.harvard.mgh.purcell.gPLINK2.forms
CCAssoc(GPLINK)
- Constructor for class edu.harvard.mgh.purcell.gPLINK2.forms.
CCAssoc
ccButton
- Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
Clustering
ccFilterButton
- Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.
FilterDialog
ccFilterCBox
- Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.
FilterDialog
CELL_DEFAULT
- Static variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
CCAssoc
cellButton
- Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
CCAssoc
changeFromTo
- Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.
FilterDialog
changeTransitFile(String[], boolean)
- Method in class edu.harvard.mgh.purcell.gCLINE.
StartFrame
Tell the file transfur status that there is a change in the files being transfered.
checkButtons()
- Method in class edu.harvard.mgh.purcell.gPLINK2.
PLINK_Open
Enable the ok and remote browse buttons as appropreate.
checkFields
- Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.
InputPane
checkValid()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
Merge.BinSelectPanel
checkValid()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
Merge.ListSelectPanel
checkValid()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
Merge.TextSelectPanel
childrenFile(String[], DefaultMutableTreeNode)
- Method in class edu.harvard.mgh.purcell.gCLINE.
HierarchyDialog
childrenOp(String, DefaultMutableTreeNode)
- Method in class edu.harvard.mgh.purcell.gCLINE.
HierarchyDialog
chooser
- Variable in class edu.harvard.mgh.purcell.gPLINK2.
OpenHapDialog.myActionListener
A GCFileChooser that selects the file
chrButton
- Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.
FilterDialog
chrCBox
- Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.
FilterDialog
CI_DEFAULT
- Static variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
AlleleAssoc
The default ci parameter is 0.95
CI_DEFAULT
- Static variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
CCAssoc
CI_DEFAULT
- Static variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
FamAssoc
CI_DEFAULT
- Static variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
StratAnaly
ciButton
- Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
AlleleAssoc
Flag the ci option
ciButton
- Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
CCAssoc
ciButton
- Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
FamAssoc
ciButton
- Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
StratAnaly
ciText
- Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
AlleleAssoc
Allow the user to set the --ci parameter
ciText
- Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
CCAssoc
ciText
- Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
FamAssoc
ciText
- Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
StratAnaly
cline
- Variable in class edu.harvard.mgh.purcell.gCLINE.data.
OperationInfo
A String that holds the command line for this operation.
cline
- Variable in class edu.harvard.mgh.purcell.gPLINK2.
AddGenericOp
The JTextField that holds the commandline
CLINE_KEY
- Static variable in interface edu.harvard.mgh.purcell.gCLINE.data.
KeyWords
key word for the command line attributes
clineText
- Variable in class edu.harvard.mgh.purcell.gCLINE.
EditOpDialog
close
- Variable in class edu.harvard.mgh.purcell.gCLINE.
EditFolderDialog
closeButtons()
- Method in class edu.harvard.mgh.purcell.gPLINK2.baseForm.
Form
closeDialog
- Variable in class edu.harvard.mgh.purcell.gCLINE.
EditOpDialog
closeForm
- Variable in class edu.harvard.mgh.purcell.gPLINK2.
AddGenericOp
Close everything up nicely
closing
- Variable in class edu.harvard.mgh.purcell.gCLINE.
StartFrame
An ActionListener that closers the gui.
Clustering
- Class in
edu.harvard.mgh.purcell.gPLINK2.forms
Form for the clustering command --cluster
Clustering(GPLINK)
- Constructor for class edu.harvard.mgh.purcell.gPLINK2.forms.
Clustering
create a show a new Clustering Form
command
- Variable in class edu.harvard.mgh.purcell.gCLINE.data.
RunCommand
command
- Variable in class edu.harvard.mgh.purcell.gCLINE.
EditOpDialog
command
- Variable in class edu.harvard.mgh.purcell.gPLINK2.
PLINK_Execute
A JTextField that holds the command we wish to pass to the computer.
COMMAND_KEY
- Static variable in interface edu.harvard.mgh.purcell.gCLINE.data.
KeyWords
command key
COMMAND_PREFIX_KEY
- Static variable in interface edu.harvard.mgh.purcell.gCLINE.data.
KeyWords
PLINK prefix key
COMPLETE
- Static variable in class edu.harvard.mgh.purcell.gCLINE.data.
AutoUpdater
Flags a completed operation
config
- Variable in class edu.harvard.mgh.purcell.gPLINK2.
PlinkMenuBar
Configure
- Class in
edu.harvard.mgh.purcell.gCLINE.general
Configure local and remote parameters.
Configure(Record)
- Constructor for class edu.harvard.mgh.purcell.gCLINE.general.
Configure
Create a configuration dialog that edits the configuration of the current record.
conn
- Variable in class edu.harvard.mgh.purcell.gCLINE.data.
Record
A String that holds the ssh connection.
conn
- Variable in class edu.harvard.mgh.purcell.gCLINE.data.
RunCommand
conn
- Variable in class edu.harvard.mgh.purcell.gCLINE.general.
GCFileChooser
conn
- Variable in class edu.harvard.mgh.purcell.gCLINE.tester.
Open
conn
- Variable in class edu.harvard.mgh.purcell.gPLINK2.
PLINK_Open
A SshClient that is used to open the remote browser.
connect()
- Method in class edu.harvard.mgh.purcell.gCLINE.data.
Record
connect(ErrorManager, JFrame, String, String, int)
- Static method in class edu.harvard.mgh.purcell.gCLINE.data.
Record
Connect the ssh client.
countButton
- Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
AlleleFreq
Buttons that allow the user to select the --count
covarButton
- Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
Regression
covarField
- Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
Regression
coverFile
- Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
QuantTrtInt
The covarienance file associated with this test
create()
- Method in class edu.harvard.mgh.purcell.gPLINK2.baseForm.
FilterDialog
createAltEditor()
- Method in class edu.harvard.mgh.purcell.gCLINE.general.
Configure
Create a JPanel that contains alternative editor
createAltPheno()
- Method in class edu.harvard.mgh.purcell.gPLINK2.baseForm.
InputPane
Create a JPanel that contains the alternative phenotype options.
createBinary()
- Method in class edu.harvard.mgh.purcell.gPLINK2.baseForm.
InputPane
Create a JPanel that has the binary input options.
createBinary()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
Merge.BinSelectPanel
createBody()
- Method in class edu.harvard.mgh.purcell.gPLINK2.baseForm.
Form
Create the body for this form.
createBody()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
AlleleAssoc
create the body specific to this form.
createBody()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
AlleleFreq
Create the body for this form.
createBody()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
Basic
createBody()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
CCAssoc
createBody()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
Clustering
create the body of the form
createBody()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
FamAssoc
createBody()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
GenFileSet
createBody()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
HapCCAssoc
createBody()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
HaploFreq
createBody()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
HaploPhase
createBody()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
HapTDTAssoc
createBody()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
HardyWinEq
createBody()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
HomozRuns
createBody()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
IBSdist
createBody()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
IndHetz
createBody()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
MendelErr
createBody()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
Merge
createBody()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
Missing
createBody()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
NearNeigh
createBody()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
QuantTrtInt
createBody()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
Regression
createBody()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
SetAssoc
createBody()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
StratAnaly
createBody()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
Validate
createButton()
- Method in class edu.harvard.mgh.purcell.gCLINE.general.
Configure
Create a panel that has both the ok and cancel buttons.
createButton()
- Method in class edu.harvard.mgh.purcell.gCLINE.general.
GCFileChooser
Create a button panel for the remote dialog.
createButton()
- Method in class edu.harvard.mgh.purcell.gCLINE.tester.
Open
Create a panel to hold the butttons.
createButton()
- Method in class edu.harvard.mgh.purcell.gPLINK2.
PLINK_Open
Create a panel to hold the butttons.
createButtonPane()
- Method in class edu.harvard.mgh.purcell.gCLINE.
LinkNewFileDialog
Create a panel to hold the ok/cancel buttons.
createButtonPane()
- Method in class edu.harvard.mgh.purcell.gPLINK2.baseForm.
Form
Create a JPanel that holds the ok/cancel buttons for this form.
createButtons()
- Method in class edu.harvard.mgh.purcell.gCLINE.
EditFolderDialog
createButtons()
- Method in class edu.harvard.mgh.purcell.gPLINK2.
PLINK_Import
Create the JButtons for this form.
createButtonsPanel()
- Method in class edu.harvard.mgh.purcell.gCLINE.
DeleteOpDialog
Create a JPanel that holds the buttons for this dialog.
createConnection()
- Method in class edu.harvard.mgh.purcell.gCLINE.tester.
Open
Create a panel that holds the connection information.
createConnection()
- Method in class edu.harvard.mgh.purcell.gPLINK2.
PLINK_Open
Create a panel that holds the connection information.
createContent(DefaultListModel)
- Method in class edu.harvard.mgh.purcell.gCLINE.general.
GCFileChooser
createError(String, String)
- Method in class edu.harvard.mgh.purcell.gCLINE.general.
ErrorManager
Create an error message with a citation.
createExicute()
- Method in class edu.harvard.mgh.purcell.gCLINE.
PopUpMenu
createExicute()
- Method in class edu.harvard.mgh.purcell.gCLINE.tester.
TestFrame.myPopUpMenu
createExicute()
- Method in class edu.harvard.mgh.purcell.gPLINK2.
GPLINK.myPopUpMenu
createFileList()
- Method in class edu.harvard.mgh.purcell.gCLINE.general.
GCFileChooser
createFilePane()
- Method in class edu.harvard.mgh.purcell.gCLINE.
LinkNewFileDialog
Create the panel that holds the file text box and corrisponding browse button.
createFilePanel(String[], boolean)
- Method in class edu.harvard.mgh.purcell.gCLINE.
DeleteOpDialog
Find files attached to all the operaitons and initalize the appropreate panels.
createFiles()
- Method in class edu.harvard.mgh.purcell.gCLINE.
EditFolderDialog
createFormsMenu()
- Method in class edu.harvard.mgh.purcell.gCLINE.tester.
MenuBarMain
Create the menu for command specific forms.
createFormsMenu()
- Method in class edu.harvard.mgh.purcell.gPLINK2.
PlinkMenuBar
Create the menu for command specific forms.
createFormSpecific()
- Method in class edu.harvard.mgh.purcell.gCLINE.general.
Configure
createFormSpecific()
- Method in class edu.harvard.mgh.purcell.gCLINE.tester.
TestFrame.StartFrameConfig
createFormSpecific()
- Method in class edu.harvard.mgh.purcell.gPLINK2.
PLINK_Config
Layout the PLINK configuration fields.
createHaplo()
- Method in class edu.harvard.mgh.purcell.gPLINK2.
PLINK_Config
Layout the haploview configuration field.
createImageIcon(String)
- Method in class edu.harvard.mgh.purcell.gPLINK2.
GPLINK.myOpView
Intelligently create an image URL
createInOutPane()
- Method in class edu.harvard.mgh.purcell.gCLINE.
LinkNewFileDialog
Create a JPanel that allows the user to select the file as either an input or output file.
createLocal()
- Method in class edu.harvard.mgh.purcell.gCLINE.tester.
Open
Create the panel that holds the local project field and associated button.
createLocal()
- Method in class edu.harvard.mgh.purcell.gPLINK2.
PLINK_Open
Create the panel that holds the local project field and associated button.
createMergeTarget()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
Merge
createMessage(String, String)
- Method in class edu.harvard.mgh.purcell.gCLINE.general.
ErrorManager
Create a message with a citation.
createOpPanel(String[])
- Method in class edu.harvard.mgh.purcell.gCLINE.
DeleteOpDialog
Creat a Panel that has all the operation names with the check box to flag confirmation of deletion
createOptions()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
Merge
createPanel()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
Merge.ListSelectPanel
createPanel()
- Method in class edu.harvard.mgh.purcell.gPLINK2.
OpenHapDialog
Intialize and layout the panel.
createPlink()
- Method in class edu.harvard.mgh.purcell.gPLINK2.
PLINK_Config
Layout the plink configuration fields.
createPopUp(StartFrame, Record, String[], String[])
- Method in class edu.harvard.mgh.purcell.gCLINE.pane.
FolderView
createPopUp(StartFrame, Record, String[], String[])
- Method in class edu.harvard.mgh.purcell.gCLINE.pane.
OpView
createPopUp(StartFrame, Record, String[], String[])
- Method in class edu.harvard.mgh.purcell.gCLINE.tester.
TestFrame.myFolderView
createPopUp(StartFrame, Record, String[], String[])
- Method in class edu.harvard.mgh.purcell.gCLINE.tester.
TestFrame.myOpView
createPopUp(StartFrame, Record, String[], String[])
- Method in class edu.harvard.mgh.purcell.gPLINK2.
GPLINK.myFolderView
createPopUp(StartFrame, Record, String[], String[])
- Method in class edu.harvard.mgh.purcell.gPLINK2.
GPLINK.myOpView
createProjectMenu()
- Method in class edu.harvard.mgh.purcell.gCLINE.tester.
MenuBarMain
Create the menu for general project operatoins.
createProjectMenu()
- Method in class edu.harvard.mgh.purcell.gPLINK2.
PlinkMenuBar
Create the menu for general project operatoins.
createRecodeOps()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
Merge
createRemote()
- Method in class edu.harvard.mgh.purcell.gCLINE.tester.
Open
Create a panel that holds the remote project name.
createRemote()
- Method in class edu.harvard.mgh.purcell.gPLINK2.
PLINK_Open
Create a panel that holds the remote project name.
createRemoteFlag()
- Method in class edu.harvard.mgh.purcell.gCLINE.tester.
Open
Create a panel to hold the remote flag.
createRemoteFlag()
- Method in class edu.harvard.mgh.purcell.gPLINK2.
PLINK_Open
Create a panel to hold the remote flag.
createRoots()
- Method in class edu.harvard.mgh.purcell.gPLINK2.
PLINK_Import
Create a JPanel that contains the JComboBox with the appropreate file root options.
createStd()
- Method in class edu.harvard.mgh.purcell.gPLINK2.baseForm.
InputPane
Create JPanel that contains the options for a standard text input files.
createStd()
- Method in class edu.harvard.mgh.purcell.gPLINK2.forms.
Merge.TextSelectPanel
createTree()
- Method in class edu.harvard.mgh.purcell.gCLINE.
HierarchyDialog
createUpdate()
- Method in class edu.harvard.mgh.purcell.gCLINE.general.
Configure
cText
- Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
CCAssoc
currentDir
- Variable in class edu.harvard.mgh.purcell.gCLINE.general.
GCFileChooser
currentFile
- Variable in class edu.harvard.mgh.purcell.gCLINE.pane.
FileView
Overview
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