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

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
 

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