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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 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
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
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
getSavedBrowse()
- Static method in class edu.harvard.mgh.purcell.gCLINE.data.
Record
Get the what browse option is saved in the global config file.
getStatusExt()
- Method in class edu.harvard.mgh.purcell.gCLINE.data.
Record
Get the log extention
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.
getUpdateSec()
- Method in class edu.harvard.mgh.purcell.gCLINE.data.
Record
GLOBAL_CONFIG
- Static variable in interface edu.harvard.mgh.purcell.gCLINE.data.
KeyWords
globalConfig
- Variable in class edu.harvard.mgh.purcell.gCLINE.data.
Record
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
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
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