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ok - Variable in class edu.harvard.mgh.purcell.gCLINE.EditFolderDialog
 
ok - Variable in class edu.harvard.mgh.purcell.gCLINE.EditOpDialog
 
ok - Variable in class edu.harvard.mgh.purcell.gPLINK2.AddGenericOp
A JButton that signals the form is complete
ok - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.Form
The ok button on the form, this is a class variable because it is en/disabled in okForm()
ok - Variable in class edu.harvard.mgh.purcell.gPLINK2.OpenHapDialog
A JButton that signals to process and close the dialog.
ok - Variable in class edu.harvard.mgh.purcell.gPLINK2.PLINK_Open
 
okButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.FilterDialog
 
okButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.ThresholdDialog
Buttons to operate this dialog
okForm() - Method in class edu.harvard.mgh.purcell.gPLINK2.baseForm.Form
Enable and disable the ok button to reflect if the form is correctly or incorrectly filled out.
okInput() - Method in class edu.harvard.mgh.purcell.gPLINK2.baseForm.InputPane
Check to see if the form is filled out correctly.
okOutput() - Method in class edu.harvard.mgh.purcell.gPLINK2.baseForm.OutputPane
 
oldname - Variable in class edu.harvard.mgh.purcell.gCLINE.EditOpDialog
 
onDeniedHost(String) - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record.myHostKeyValidator
 
onHostKeyMismatch(String, String, String) - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record.myHostKeyValidator
 
onlyDir - Variable in class edu.harvard.mgh.purcell.gCLINE.general.GCFileChooser
 
onlyLocal - Variable in class edu.harvard.mgh.purcell.gCLINE.general.GCFileChooser
Flag file we are looking for as local or remote.
onUnknownHost(String, String) - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record.myHostKeyValidator
 
op1 - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Merge
 
op2 - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Merge
 
op3 - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Merge
 
op4 - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Merge
 
op5 - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Merge
 
op6 - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Merge
 
op7 - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Merge
 
OP_KEY - Static variable in interface edu.harvard.mgh.purcell.gCLINE.data.KeyWords
key word for the operations nodes
OP_LOG_EXT - Variable in class edu.harvard.mgh.purcell.gCLINE.data.Record
OP_LOG_EXT is a String that identifies the file extention for the operation log file.
op_log_ext - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.OutputPane
The extention for the operation log files
op_status_ext - Variable in class edu.harvard.mgh.purcell.gCLINE.data.AutoUpdater
The file extention that this updater looks at to determine the exit status of the log.
opDisc - Variable in class edu.harvard.mgh.purcell.gPLINK2.AddGenericOp
The JTextField that holds the operation discription
Open - Class in edu.harvard.mgh.purcell.gCLINE.tester
A dialog that opens a new project.
Open(TestFrame) - Constructor for class edu.harvard.mgh.purcell.gCLINE.tester.Open
Create a dialog that will open up a new project and establish an ssh connection.
Open(TestFrame, String) - Constructor for class edu.harvard.mgh.purcell.gCLINE.tester.Open
 
Open.gCLINEFilter - Class in edu.harvard.mgh.purcell.gCLINE.tester
A FileFilter that will look for directories
Open.gCLINEFilter() - Constructor for class edu.harvard.mgh.purcell.gCLINE.tester.Open.gCLINEFilter
 
openAlt - Variable in class edu.harvard.mgh.purcell.gCLINE.PopUpMenu
Launch the user specified file viewer.
openButtons() - Method in class edu.harvard.mgh.purcell.gPLINK2.baseForm.Form
 
openDefault - Variable in class edu.harvard.mgh.purcell.gCLINE.PopUpMenu
Launch the default file viewer
OpenHapDialog - Class in edu.harvard.mgh.purcell.gPLINK2
A JDialog that launches Haploview.
OpenHapDialog(GPLINK, String, String) - Constructor for class edu.harvard.mgh.purcell.gPLINK2.OpenHapDialog
Create a Dialog to open a Haploview instance.
OpenHapDialog.myActionListener - Class in edu.harvard.mgh.purcell.gPLINK2
Create a generic ActionListener for a browse button that launches a local file browse.
OpenHapDialog.myActionListener(JTextField, String[], String) - Constructor for class edu.harvard.mgh.purcell.gPLINK2.OpenHapDialog.myActionListener
Create myActionListener.
openHaplo - Variable in class edu.harvard.mgh.purcell.gPLINK2.OpenHapDialog
An ActionListener that attaches to the ok button and opens an instance of haploview using the files specified in the dialog.
openHaploview() - Method in class edu.harvard.mgh.purcell.gPLINK2.GPLINK.myPopUpMenu
 
OperationInfo - Class in edu.harvard.mgh.purcell.gCLINE.data
A class that contains the information for a given operation.
OperationInfo() - Constructor for class edu.harvard.mgh.purcell.gCLINE.data.OperationInfo
 
OperationInfo(String, String, String, String) - Constructor for class edu.harvard.mgh.purcell.gCLINE.data.OperationInfo
 
operations - Variable in class edu.harvard.mgh.purcell.gCLINE.DeleteOpDialog
A JCheckBox array that holds the deletion options for the selected opertaions.
opName - Variable in class edu.harvard.mgh.purcell.gCLINE.HierarchyDialog
 
opName - Variable in class edu.harvard.mgh.purcell.gCLINE.LinkNewFileDialog
A String that identifies the operation you want to link the file to.
opName - Variable in class edu.harvard.mgh.purcell.gPLINK2.AddGenericOp
The JTextField that holds the operation name
opnames - Variable in class edu.harvard.mgh.purcell.gCLINE.PopUpMenu
An array of the operation names
opStatis - Variable in class edu.harvard.mgh.purcell.gCLINE.data.AutoUpdater
A hash map that keeps all the operations and their current status completed, running, or failed.
optional - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Merge
 
OpView - Class in edu.harvard.mgh.purcell.gCLINE.pane
Look at the operation tree.
OpView(Record, FileView) - Constructor for class edu.harvard.mgh.purcell.gCLINE.pane.OpView
Create an operation view
opViewer - Variable in class edu.harvard.mgh.purcell.gCLINE.StartFrame
A panel to look at the operation tree.
OUTFILE_KEY - Static variable in interface edu.harvard.mgh.purcell.gCLINE.data.KeyWords
key word for the output file group
outfileLabel - Variable in class edu.harvard.mgh.purcell.gCLINE.EditOpDialog
 
outfiles - Variable in class edu.harvard.mgh.purcell.gCLINE.DeleteOpDialog
A JCheckBox array that holds the deletion options for the selected output files.
outfiles - Variable in class edu.harvard.mgh.purcell.gPLINK2.AddGenericOp
A list that holds all the current output files
outfileText - Variable in class edu.harvard.mgh.purcell.gCLINE.EditOpDialog
 
outlistmodel - Variable in class edu.harvard.mgh.purcell.gPLINK2.AddGenericOp
A DefaultListModel that holds the data for the output list
output - Variable in class edu.harvard.mgh.purcell.gCLINE.data.OperationInfo
A DefaultMutableTreeNode that holds the output files.
output - Variable in class edu.harvard.mgh.purcell.gCLINE.EditOpDialog
 
output - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.Form
The OutputPane for this form.
outputLines - Variable in class edu.harvard.mgh.purcell.gCLINE.data.RunCommand
 
OutputPane - Class in edu.harvard.mgh.purcell.gPLINK2.baseForm
 
OutputPane(Form, String, Vector<String>, String) - Constructor for class edu.harvard.mgh.purcell.gPLINK2.baseForm.OutputPane
 

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