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

S

save - Variable in class edu.harvard.mgh.purcell.gPLINK2.PlinkMenuBar
 
saveConfig() - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
Save the config values
saveInfo() - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
 
saveInfo(File) - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
Write the information to the project file of the xml format.
saveRemoteConfig() - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
 
saveRemoteConfig() - Method in class edu.harvard.mgh.purcell.gCLINE.tester.TestFrame.myProject
 
saveRemoteConfig() - Method in class edu.harvard.mgh.purcell.gPLINK2.data.Project
 
setAltEditor(String) - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
Set the alternative editor
SetAssoc - Class in edu.harvard.mgh.purcell.gPLINK2.forms
A Set based association file.
SetAssoc(GPLINK) - Constructor for class edu.harvard.mgh.purcell.gPLINK2.forms.SetAssoc
Create the set based association form.
setAutoUpdater(AutoUpdater) - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
This is mainly abstract to remind programers to initalize it
setAutoUpdater(AutoUpdater) - Method in class edu.harvard.mgh.purcell.gCLINE.tester.TestFrame.myProject
 
setAutoUpdater(AutoUpdater) - Method in class edu.harvard.mgh.purcell.gPLINK2.data.Project
 
setBrowse - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.SetAssoc
 
setBrowseOnly(boolean) - Method in class edu.harvard.mgh.purcell.gCLINE.StartFrame
 
setBrowseOnly(boolean) - Method in class edu.harvard.mgh.purcell.gCLINE.tester.TestFrame
 
setBrowseOnly(boolean) - Method in class edu.harvard.mgh.purcell.gPLINK2.GPLINK
 
setButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.FilterDialog
 
setButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.SetAssoc
 
setConnData(SshClient, String, String, String) - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
Set the connection data
setDisc - Variable in class edu.harvard.mgh.purcell.gCLINE.EditFolderDialog
 
setEnabledMenu() - Method in class edu.harvard.mgh.purcell.gPLINK2.PlinkMenuBar
 
setField - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.FilterDialog
 
setFields - Variable in class edu.harvard.mgh.purcell.gPLINK2.OpenHapDialog
An ItemListener to set the JTextFields and JButtons to reflect the corrisponding radio button selection.
setFileViewer(File) - Method in class edu.harvard.mgh.purcell.gCLINE.StartFrame
Set the log file viewer.
setGlobalDisc(String) - Method in class edu.harvard.mgh.purcell.gCLINE.data.FileInfo
Set the global discription for this file.
setGlobalFileDisc(String, String) - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
Set a global file discriptor
setHaploAppend(String) - Method in class edu.harvard.mgh.purcell.gPLINK2.data.Project
 
setHaploPath(String) - Method in class edu.harvard.mgh.purcell.gPLINK2.data.Project
 
setLastProject() - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
Add the current project to our list so that we can launch the recent projects quickly from the associated menu bar.
setLocalDisc(String) - Method in class edu.harvard.mgh.purcell.gCLINE.data.FileInfo
Set the local discription for this file.
setLog(String) - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
Set the log extention
setMaxButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.SetAssoc
 
setMaxText - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.SetAssoc
 
setMinButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.SetAssoc
 
setMinText - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.SetAssoc
 
setP1(String) - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
Set the first project name if it's not equal to null.
setP2(String) - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
Set the second project name if it's not equal to null
setP3(String) - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
Set the third project name if it's not equal to null
setP4(String) - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
Set the forth project name if it's not equal to null
setPlinkPath(String) - Method in class edu.harvard.mgh.purcell.gPLINK2.data.Project
 
setPlinkPrefix(String) - Method in class edu.harvard.mgh.purcell.gPLINK2.data.Project
 
setSavedBrowse() - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
 
setStatus(String) - Method in class edu.harvard.mgh.purcell.gCLINE.StartFrame
Set the file transet status message.
setStuff() - Method in class edu.harvard.mgh.purcell.gPLINK2.forms.FamAssoc
 
setText - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.SetAssoc
 
setUpdateSec(int) - Method in class edu.harvard.mgh.purcell.gCLINE.data.Record
 
setVersion() - Method in class edu.harvard.mgh.purcell.gCLINE.StartFrame
Set the version number.
setVersion() - Method in class edu.harvard.mgh.purcell.gCLINE.tester.TestFrame
 
setVersion() - Method in class edu.harvard.mgh.purcell.gPLINK2.GPLINK
 
sexFilterButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.FilterDialog
 
sexFilterCBox - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.FilterDialog
 
sgButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.FilterDialog
 
showChooser() - Method in class edu.harvard.mgh.purcell.gCLINE.general.GCFileChooser
Show the file chooser.
showHierachyFile - Variable in class edu.harvard.mgh.purcell.gCLINE.PopUpMenu
 
showHierachyOp - Variable in class edu.harvard.mgh.purcell.gCLINE.PopUpMenu
 
SNPButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.OpenHapDialog
A JButton to browse for SNP defined files.
SNPField - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.FilterDialog
 
SNPFile - Variable in class edu.harvard.mgh.purcell.gPLINK2.OpenHapDialog
A JTextField that holds a SNP defined file name.
SNPRB - Variable in class edu.harvard.mgh.purcell.gPLINK2.OpenHapDialog
A JRadioButton to flag the SNP file option
SNPSuffex - Static variable in class edu.harvard.mgh.purcell.gPLINK2.OpenHapDialog
A String array that holds all the suffix's that flag a SNP file.
StartFrame - Class in edu.harvard.mgh.purcell.gCLINE
General main window for the generalized command line gui.
StartFrame(String) - Constructor for class edu.harvard.mgh.purcell.gCLINE.StartFrame
Create a GUI.
StartFrame.Download - Class in edu.harvard.mgh.purcell.gCLINE
Download a set of files from a remote directory.
StartFrame.Download(Record, boolean, File, String[]) - Constructor for class edu.harvard.mgh.purcell.gCLINE.StartFrame.Download
Create A Download instance.
StartFrame.Upload - Class in edu.harvard.mgh.purcell.gCLINE
Upload a set of files to a remote directory.
StartFrame.Upload(Record, boolean, String, File[]) - Constructor for class edu.harvard.mgh.purcell.gCLINE.StartFrame.Upload
Create A Upload instance.
statusBar - Variable in class edu.harvard.mgh.purcell.gCLINE.StartFrame
A label that informs weather files are in transit from or to a remote directory, this is shown at the lower right hand side.
stdCheck - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.InputPane
A JCheckBox that flags the short standard input format (--file fileroot)
stdCheck - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Merge.TextSelectPanel
 
stdShort - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.InputPane
A JComboBox that holds the file root options for the short standard input format
stdShort - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Merge.TextSelectPanel
 
stealLock() - Method in class edu.harvard.mgh.purcell.gCLINE.data.Lock
 
StratAnaly - Class in edu.harvard.mgh.purcell.gPLINK2.forms
 
StratAnaly(GPLINK) - Constructor for class edu.harvard.mgh.purcell.gPLINK2.forms.StratAnaly
 
stripAndSplit(String) - Static method in class edu.harvard.mgh.purcell.gCLINE.data.RunCommand
Split a given strip up into an array based on the spaces outside of "".
sucessIcon - Variable in class edu.harvard.mgh.purcell.gCLINE.data.AutoUpdater.MyRenderer
 
suffex - Variable in class edu.harvard.mgh.purcell.gCLINE.LinkNewFileDialog.BrowseButton
 
suffex - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.FilterDialog.BrowseButton
 
suffex - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.Form.BrowseButton
 
suffexDisc - Variable in class edu.harvard.mgh.purcell.gCLINE.LinkNewFileDialog.BrowseButton
 
suffexDisc - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.FilterDialog.BrowseButton
 
suffexDisc - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.Form.BrowseButton
 
suffix - Variable in class edu.harvard.mgh.purcell.gPLINK2.OpenHapDialog.myActionListener
A String array that holds the suffix of the files we are looking for
swapOpDown - Variable in class edu.harvard.mgh.purcell.gCLINE.pane.OpView
Move the selected node up the tree.
swapOpUp - Variable in class edu.harvard.mgh.purcell.gCLINE.pane.OpView
Move the selected node down the tree.
swButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.FilterDialog
 

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