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maf - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.ThresholdDialog
Fields for user entered thresholds
MAF_DEFAULT - Static variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.ThresholdDialog
The default minor allelic frequency
mafButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.ThresholdDialog
Buttons to flag user specified thresholds
main(String[]) - Static method in class edu.harvard.mgh.purcell.gCLINE.data.FileInfo
 
main(String[]) - Static method in class edu.harvard.mgh.purcell.gCLINE.tester.TestFrame
The main fuction that is where it all starts
main(String[]) - Static method in class edu.harvard.mgh.purcell.gPLINK2.GPLINK
The main fuction that is where it all starts
makeBin - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.GenFileSet
 
makeBin - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Merge
 
makeVisible() - Method in class edu.harvard.mgh.purcell.gCLINE.general.Configure
 
mapBrowse - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.InputPane
A BrowseButton that selects the map file.
mapBrowse - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Merge.TextSelectPanel
 
mapButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.OpenHapDialog
A JButton that triggers a browse for the map/bim file.
mapField - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.InputPane
A JTextField that holds the map file name.
mapField - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Merge.TextSelectPanel
 
mapFile - Variable in class edu.harvard.mgh.purcell.gPLINK2.OpenHapDialog
A JTextField that holds the map/bim file names.
mapSuffex - Static variable in class edu.harvard.mgh.purcell.gPLINK2.OpenHapDialog
A String array that holds all the suffix's that flag a map/bim file.
matButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.FamAssoc
 
matchBrowse - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Clustering
 
matchButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Clustering
 
matchTBrowse - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Clustering
 
matchTButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Clustering
 
matchText - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Clustering
 
matchTText - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Clustering
 
max_line_length - Static variable in class edu.harvard.mgh.purcell.gCLINE.general.ErrorManager
The maximum number of characters per line.
maxMaf - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.ThresholdDialog
Fields for user entered thresholds
MAXMAF_DEFAULT - Static variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.ThresholdDialog
The default maximum minor allelic frequency
maxMafButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.ThresholdDialog
Buttons to flag user specified thresholds
mBestButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.CCAssoc
 
mcButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Clustering
 
mcc1Text - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Clustering
 
mcc2Text - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Clustering
 
mccButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Clustering
 
mcText - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Clustering
 
mDomButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.CCAssoc
 
MendelErr - Class in edu.harvard.mgh.purcell.gPLINK2.forms
 
MendelErr(GPLINK) - Constructor for class edu.harvard.mgh.purcell.gPLINK2.forms.MendelErr
 
mendell - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.ThresholdDialog
Fields for user entered thresholds
mendell2 - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.ThresholdDialog
Fields for user entered thresholds
mendellButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.ThresholdDialog
Buttons to flag user specified thresholds
menu - Variable in class edu.harvard.mgh.purcell.gPLINK2.GPLINK
The menu bar for our gPLINK window.
MenuBarMain - Class in edu.harvard.mgh.purcell.gCLINE.tester
Create a menu bar that will hold both the general project menu and the command specific forms.
MenuBarMain(TestFrame, Configure) - Constructor for class edu.harvard.mgh.purcell.gCLINE.tester.MenuBarMain
 
Merge - Class in edu.harvard.mgh.purcell.gPLINK2.forms
Merge two file sets.
Merge(GPLINK) - Constructor for class edu.harvard.mgh.purcell.gPLINK2.forms.Merge
 
Merge.BinSelectPanel - Class in edu.harvard.mgh.purcell.gPLINK2.forms
 
Merge.BinSelectPanel(GPLINK) - Constructor for class edu.harvard.mgh.purcell.gPLINK2.forms.Merge.BinSelectPanel
 
Merge.ListSelectPanel - Class in edu.harvard.mgh.purcell.gPLINK2.forms
 
Merge.ListSelectPanel(GPLINK) - Constructor for class edu.harvard.mgh.purcell.gPLINK2.forms.Merge.ListSelectPanel
 
Merge.TextSelectPanel - Class in edu.harvard.mgh.purcell.gPLINK2.forms
 
Merge.TextSelectPanel(GPLINK) - Constructor for class edu.harvard.mgh.purcell.gPLINK2.forms.Merge.TextSelectPanel
 
mergeInputs - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Merge
 
messanger - Variable in class edu.harvard.mgh.purcell.gCLINE.StartFrame
The error manager for this gui.
META_FILE - Static variable in interface edu.harvard.mgh.purcell.gCLINE.data.KeyWords
String that identifies the file extention for
mfilterField - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.FilterDialog
 
mGenButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.CCAssoc
 
mh2Button - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.StratAnaly
 
mhButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.StratAnaly
 
mind - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.ThresholdDialog
Fields for user entered thresholds
MIND_DEFAULT - Static variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.ThresholdDialog
The default maximum per-person missing
mindButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.ThresholdDialog
Buttons to flag user specified thresholds
mishapNum - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Missing
A JTextField holding the --mishap-window arguemnt.
Missing - Class in edu.harvard.mgh.purcell.gPLINK2.forms
Create a Form to test for missing data using PLINK "--missing".
Missing(GPLINK) - Constructor for class edu.harvard.mgh.purcell.gPLINK2.forms.Missing
Create a Missing form.
mpButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.SetAssoc
 
mperm2Button - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.CCAssoc
 
mperm2Text - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.CCAssoc
 
MPERM_DEFAULT - Static variable in class edu.harvard.mgh.purcell.gPLINK2.forms.AlleleAssoc
The default mperm perameter is 1000
MPERM_DEFAULT - Static variable in class edu.harvard.mgh.purcell.gPLINK2.forms.CCAssoc
 
MPERM_DEFAULT - Static variable in class edu.harvard.mgh.purcell.gPLINK2.forms.FamAssoc
 
mpermButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.AlleleAssoc
Flag the --mperm option
mpermButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.FamAssoc
 
mpermText - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.AlleleAssoc
Allow the user to set the --mperm perameter
mpermText - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.FamAssoc
 
mphenoText - Variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.InputPane
A JTextField that contains the column you wish to use on the alternative pheotype file.
mpText - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.SetAssoc
 
mRecButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.CCAssoc
 
mTrendButton - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.CCAssoc
 
my_alignment - Static variable in class edu.harvard.mgh.purcell.gPLINK2.baseForm.InputPane
 
my_alignment - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Merge.BinSelectPanel
 
my_alignment - Variable in class edu.harvard.mgh.purcell.gPLINK2.forms.Merge.TextSelectPanel
 
myArrayString(String[]) - Method in class edu.harvard.mgh.purcell.gCLINE.HierarchyDialog
 
myConfig - Variable in class edu.harvard.mgh.purcell.gCLINE.tester.MenuBarMain
 
myLock - Variable in class edu.harvard.mgh.purcell.gCLINE.data.Record
Locking information for the folder
myTree - Variable in class edu.harvard.mgh.purcell.gCLINE.pane.OpView
JTree to show the Record

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