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

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
Create a BrowseButton for this form.
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
 
advplink - Variable in class edu.harvard.mgh.purcell.gPLINK2.PlinkMenuBar
 
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
 

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