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

G

GCFileChooser - Class in edu.harvard.mgh.purcell.gCLINE.general
This class launches dailogs that allow the user to pick files on either a remote or local computer.
GCFileChooser(JFrame, FileFilter, boolean, boolean, SshClient, String) - Constructor for class edu.harvard.mgh.purcell.gCLINE.general.GCFileChooser
Create an instance of our custom file chooser.
GCFileChooser(JDialog, FileFilter, boolean, boolean, SshClient, String) - Constructor for class edu.harvard.mgh.purcell.gCLINE.general.GCFileChooser
Create an instance of our custom file chooser.
GCFileChooser.FileChoosenEvent - Class in edu.harvard.mgh.purcell.gCLINE.general
Create an EventObject to notify the selection of a file.
GCFileChooser.FileChoosenEvent(Object) - Constructor for class edu.harvard.mgh.purcell.gCLINE.general.GCFileChooser.FileChoosenEvent
 
GCFileChooser.FileChoosenListener - Interface in edu.harvard.mgh.purcell.gCLINE.general
Create an EventListener for our internally defined event.
geneField - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.FilterDialog
 
geneLable - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.FilterDialog
 
GenFileSet - Class in edu.harvard.mgh.purcell.gPLINK2.forms
Reformat a fileset.
GenFileSet(GPLINK) - Constructor for class edu.harvard.mgh.purcell.gPLINK2.forms.GenFileSet
 
geno - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.ThresholdDialog
Fields for user entered thresholds
GENO_DEFAULT - Static variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.ThresholdDialog
The default maximum per-SNP missing
genoButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.ThresholdDialog
Buttons to flag user specified thresholds
genoButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Regression
 
genomicText - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.NearNeigh
 
getAllOp() - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
Get a list of all the operations
getAltEditor() - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
Get the command for the alternative editor
getBinRoots() - Method in class edu.harvard.mgh.purcell.gPLINK2.baseForm.InputPane
Get a list of possible short binary roots.
getBrowseOnly() - Method in class edu.harvard.mgh.purcell.gCLINE.StartFrame
 
getChildOp(String) - Method in class edu.harvard.mgh.purcell.gCLINE.HierarchyDialog
 
getCline() - Method in class edu.harvard.mgh.purcell.gCLINE.data.OperationInfo
 
getCommand() - Method in class edu.harvard.mgh.purcell.gPLINK2.forms.Merge.BinSelectPanel
 
getCommand() - Method in class edu.harvard.mgh.purcell.gPLINK2.forms.Merge.ListSelectPanel
 
getCommand() - Method in class edu.harvard.mgh.purcell.gPLINK2.forms.Merge.TextSelectPanel
 
getCommandline(String) - Method in class edu.harvard.mgh.purcell.gPLINK2.PLINK_Import
Get the command line based on the log file.
getConn() - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
get the connection to the remote directory
getDescription() - Method in class edu.harvard.mgh.purcell.gCLINE.tester.Open.gCLINEFilter
Grab a valid discription of this filter.
getDescription() - Method in class edu.harvard.mgh.purcell.gPLINK2.PLINK_Open.gCLINEFilter
Grab a valid discription of this filter.
getDisc() - Method in class edu.harvard.mgh.purcell.gCLINE.data.OperationInfo
 
getDiscription() - Method in class edu.harvard.mgh.purcell.gCLINE.data.FileInfo
Get the full discription with both the global and local discription.
getFilename(String) - Method in class edu.harvard.mgh.purcell.gCLINE.pane.FolderView
 
getGlobalDisc() - Method in class edu.harvard.mgh.purcell.gCLINE.data.FileInfo
Get the global discription for the file.
getGlobalNote(String) - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
Get a specific file note
getHaploAppend() - Method in class edu.harvard.mgh.purcell.gPLINK2.data.Project
 
getHaploPath() - Method in class edu.harvard.mgh.purcell.gPLINK2.data.Project
 
getHomeFiles() - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
Get a list of files that are in your working directory
getHomeFolder() - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
Get the home folder that the data is stored in.
getInFiles(String) - Method in class edu.harvard.mgh.purcell.gCLINE.HierarchyDialog
 
getInput(String) - Method in class edu.harvard.mgh.purcell.gPLINK2.PLINK_Import
Pulls an array of strings identifing the input files
getInputFiles() - Method in class edu.harvard.mgh.purcell.gCLINE.data.OperationInfo
 
getKey() - Method in class edu.harvard.mgh.purcell.gCLINE.data.Lock
Get the key for this instance of the lock
getLocalDisc() - Method in class edu.harvard.mgh.purcell.gCLINE.data.FileInfo
Get the local discription for the file.
getLocalFolder() - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
Get the name of the local file
getLocalUpdateSec() - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
Get the local update period for the auto-updater.
getLog(File, String) - Method in class edu.harvard.mgh.purcell.gCLINE.data.OperationInfo
Get the log file associated with this operation
getLog(File, String, Vector<String[]>) - Static method in class edu.harvard.mgh.purcell.gCLINE.data.OperationInfo
 
getLogExt() - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
 
getName() - Method in class edu.harvard.mgh.purcell.gCLINE.data.OperationInfo
Get the unique name of the operation.
getOp(String) - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
Get the full information on an operation
getOpDetails() - Method in class edu.harvard.mgh.purcell.gCLINE.data.OperationInfo
Get the details of the operation like the command line.
getOutFiles(String) - Method in class edu.harvard.mgh.purcell.gCLINE.HierarchyDialog
 
getOutputFiles() - Method in class edu.harvard.mgh.purcell.gCLINE.data.OperationInfo
 
getP1() - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
Get the first project name
getP2() - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
Get the second project name
getP3() - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
Get the third project name
getP4() - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
Get the forth project name
getParentOp(String) - Method in class edu.harvard.mgh.purcell.gCLINE.HierarchyDialog
 
getPlinkPath() - Method in class edu.harvard.mgh.purcell.gPLINK2.data.Project
 
getPlinkPrefix() - Method in class edu.harvard.mgh.purcell.gPLINK2.data.Project
 
getRemoteFolder() - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
Get the name of the remote file
getRemoteUpdateSec() - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
Get the remote update period for the auto-updater.
getStdRoots() - Method in class edu.harvard.mgh.purcell.gPLINK2.baseForm.InputPane
Get a list of possible short standard roots.
getTimeStamp() - Method in class edu.harvard.mgh.purcell.gCLINE.data.OperationInfo
 
getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class edu.harvard.mgh.purcell.gCLINE.data.AutoUpdater.MyRenderer
Set the icon of each node.
GLOBAL_CONFIG - Static variable in interface edu.harvard.mgh.purcell.gCLINE.data.KeyWords
 
globalConfig - Variable in class edu.harvard.mgh.purcell.gCLINE.data.Record
globalConfig is a Properties that holds the global configuration data.
globalDisc - Variable in class edu.harvard.mgh.purcell.gCLINE.data.FileInfo
A string that holds the global discrition of this file.
globalFileNotes - Variable in class edu.harvard.mgh.purcell.gCLINE.data.Record
globalFileNotes is a HashMap that carries the global file notes.
GPLINK - Class in edu.harvard.mgh.purcell.gPLINK2
The entry class for gPLINK.
GPLINK() - Constructor for class edu.harvard.mgh.purcell.gPLINK2.GPLINK
Create a new instance of gPLINK.
GPLINK.myFolderView - Class in edu.harvard.mgh.purcell.gPLINK2
The FolderView for gPLINK.
GPLINK.myFolderView(Record) - Constructor for class edu.harvard.mgh.purcell.gPLINK2.GPLINK.myFolderView
 
GPLINK.myOpView - Class in edu.harvard.mgh.purcell.gPLINK2
An operations viewer (OpView) specific to the gPLINK window.
GPLINK.myOpView(Record, FileView) - Constructor for class edu.harvard.mgh.purcell.gPLINK2.GPLINK.myOpView
Create the OpView for a gPLINK window.
GPLINK.myPopUpMenu - Class in edu.harvard.mgh.purcell.gPLINK2
The PopUpMenu for gPLINK.
GPLINK.myPopUpMenu(StartFrame, Record, String[], String[]) - Constructor for class edu.harvard.mgh.purcell.gPLINK2.GPLINK.myPopUpMenu
 
GPLINK_EXT - Static variable in class edu.harvard.mgh.purcell.gPLINK2.data.Project
 

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