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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
Setter function for 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
Setter function for the autoUpdater.
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
Setter function for 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
This function adds the current project to the head of the list of pervious projects.
setLocalDisc(String)
- Method in class edu.harvard.mgh.purcell.gCLINE.data.
FileInfo
Set the local discription for this file.
setLocalUpdateSec(int)
- Method in class edu.harvard.mgh.purcell.gCLINE.data.
Record
Setter fuction for the local update period.
setLog(String)
- Method in class edu.harvard.mgh.purcell.gCLINE.data.
Record
Setter function for 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
Setter for the first project name.
setP2(String)
- Method in class edu.harvard.mgh.purcell.gCLINE.data.
Record
Setter for the second project name.
setP3(String)
- Method in class edu.harvard.mgh.purcell.gCLINE.data.
Record
Setter for the third project name.
setP4(String)
- Method in class edu.harvard.mgh.purcell.gCLINE.data.
Record
Setter for the forth project name.
setPlinkPath(String)
- Method in class edu.harvard.mgh.purcell.gPLINK2.data.
Project
setPlinkPrefix(String)
- Method in class edu.harvard.mgh.purcell.gPLINK2.data.
Project
setRemoteUpdateSec(int)
- Method in class edu.harvard.mgh.purcell.gCLINE.data.
Record
Setter function for the remote update period.
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
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
Overview
Package
Class
Use
Tree
Deprecated
Index
Help
PREV LETTER
NEXT LETTER
FRAMES
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All Classes
A
B
C
D
E
F
G
H
I
K
L
M
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Q
R
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T
U
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W