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A
accept(File)
- Method in class edu.harvard.mgh.purcell.gCLINE.tester.
Open.gCLINEFilter
Checks to see if the file is valid.
accept(File)
- Method in class edu.harvard.mgh.purcell.gPLINK2.
PLINK_Open.gCLINEFilter
Checks to see if the file is valid.
actionPerformed(ActionEvent)
- Method in class edu.harvard.mgh.purcell.gPLINK2.
OpenHapDialog.myActionListener
Create and show the file chooser.
addFile(String, String, String, String)
- Method in class edu.harvard.mgh.purcell.gCLINE.data.
OperationInfo
Add a file to one of the file nodes.
addFile
- Variable in class edu.harvard.mgh.purcell.gCLINE.
LinkNewFileDialog
A JTextField that holds the file name.
addFileChoosenListener(GCFileChooser.FileChoosenListener)
- Method in class edu.harvard.mgh.purcell.gCLINE.general.
GCFileChooser
Add a listener to the list.
addFileToFolder(DefaultMutableTreeNode, FileInfo)
- Method in class edu.harvard.mgh.purcell.gCLINE.data.
OperationInfo
Add a file to a given folder.
addFileToOp
- Variable in class edu.harvard.mgh.purcell.gCLINE.
PopUpMenu
addFilter(String)
- Method in class edu.harvard.mgh.purcell.gPLINK2.baseForm.
Form
AddGenericOp
- Class in
edu.harvard.mgh.purcell.gPLINK2
Create a dialog to import a non-PLINK operation.
AddGenericOp(GPLINK)
- Constructor for class edu.harvard.mgh.purcell.gPLINK2.
AddGenericOp
Create a dialog to add an operation that is not automatically processed by our plink import.
AddGenericOp.BrowseButton
- Class in
edu.harvard.mgh.purcell.gPLINK2
AddGenericOp.BrowseButton(JTextField)
- Constructor for class edu.harvard.mgh.purcell.gPLINK2.
AddGenericOp.BrowseButton
addIn
- Variable in class edu.harvard.mgh.purcell.gPLINK2.
AddGenericOp
pickAFileButton that browse to select the input files
addOp(String)
- Method in class edu.harvard.mgh.purcell.gCLINE.data.
AutoUpdater
addOp
- Variable in class edu.harvard.mgh.purcell.gPLINK2.
AddGenericOp
Add the operation to the project
addOperation(String, String, String, String, Vector<String[]>, Vector<String[]>)
- Method in class edu.harvard.mgh.purcell.gCLINE.data.
Record
Add an operation to the info document, if there is an operation of that name then replace it with this new one.
addOperation()
- Method in class edu.harvard.mgh.purcell.gPLINK2.
PLINK_Execute
Parse the command and try to add it to the GPLINK instance.
addOut
- Variable in class edu.harvard.mgh.purcell.gPLINK2.
AddGenericOp
pickAFileButton that browse to select the output files
addThreshold(String)
- Method in class edu.harvard.mgh.purcell.gPLINK2.baseForm.
Form
adjustButton
- Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
AlleleAssoc
Flag the --adjust button
adjustButton
- Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
CCAssoc
adjustButton
- Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.
StratAnaly
allBox
- Variable in class edu.harvard.mgh.purcell.gPLINK2.
PLINK_Import
A JCheckBox that flags selection of all the non-included roots.
AlleleAssoc
- Class in
edu.harvard.mgh.purcell.gPLINK2.forms
Creates a form that does a basic --assoc test
AlleleAssoc(GPLINK)
- Constructor for class edu.harvard.mgh.purcell.gPLINK2.forms.
AlleleAssoc
Create and show an allelic assocation test form.
AlleleFreq
- Class in
edu.harvard.mgh.purcell.gPLINK2.forms
Create a form that allows the user to test for Allele frequency.
AlleleFreq(GPLINK)
- Constructor for class edu.harvard.mgh.purcell.gPLINK2.forms.
AlleleFreq
creates a new Allele frequency form.
allListeners
- Variable in class edu.harvard.mgh.purcell.gCLINE.general.
GCFileChooser
Keep a vector of the listeners
allOps
- Variable in class edu.harvard.mgh.purcell.gPLINK2.
AddGenericOp
A vector of strings that contain all the operation names
altBrowse
- Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.
InputPane
A BrowseButton that selects the alternative pheotype file name.
altField
- Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.
InputPane
A JTextField that holds the alternative pheotype file name.
ancesters
- Variable in class edu.harvard.mgh.purcell.gCLINE.
HierarchyDialog
asElement(Document)
- Method in class edu.harvard.mgh.purcell.gCLINE.data.
FileInfo
Convert the information in the FileInfo to an Element.
asElement(Document)
- Method in class edu.harvard.mgh.purcell.gCLINE.data.
OperationInfo
AutoUpdater
- Class in
edu.harvard.mgh.purcell.gCLINE.data
AutoUpadater extends Timer, automatically updating the output files attached in OpView.
AutoUpdater(StartFrame, Record, String, ErrorManager, int)
- Constructor for class edu.harvard.mgh.purcell.gCLINE.data.
AutoUpdater
Create and start our unique timer.
AutoUpdater.MyRenderer
- Class in
edu.harvard.mgh.purcell.gCLINE.data
Create a renderer to reflect that status of each operation (completed, failed or running).
AutoUpdater.MyRenderer(Icon, Icon, Icon, Icon)
- Constructor for class edu.harvard.mgh.purcell.gCLINE.data.
AutoUpdater.MyRenderer
Create a new renderer
availableLock()
- Method in class edu.harvard.mgh.purcell.gCLINE.data.
Lock
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