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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
Overview
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