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InconsistentColumnNumberException - Exception in halo.data.dataExceptions
Is thrown when the number of columns containing expression values is inconsistent throughout the data file, meaning that there are RNA values missing for some probesets
InconsistentColumnNumberException() - Constructor for exception halo.data.dataExceptions.InconsistentColumnNumberException
Creates a new exception
InconsistentColumnNumberException(String) - Constructor for exception halo.data.dataExceptions.InconsistentColumnNumberException
Creates a new exception
initGui() - Method in class halo.userinterface.gui.Gui
Initialize the GUI
initialize(Data) - Method in class halo.halflife.HalfLife
initializes the HalfLife object & extracts the needed values of the Data object
initialize(Data, int) - Method in class halo.halflife.HalfLife
initializes the HalfLife object for a specific replicate of the data
initialize(Data) - Method in class halo.halflife.HalfLife_New
 
initialize(Data, int) - Method in class halo.halflife.HalfLife_New
 
initialize(Data) - Method in class halo.halflife.HalfLife_NewPre
 
initialize(Data, int) - Method in class halo.halflife.HalfLife_NewPre
 
initialize(Data) - Method in class halo.halflife.HalfLife_Pre
 
initialize(Data, int) - Method in class halo.halflife.HalfLife_Pre
 
InputHelpDialog - Class in halo.userinterface.gui.guitools
Displays a dialog with a message, a text field for user input, a help button and Enter/Cancel buttons
InputHelpDialog(Frame, String, String, String, String) - Constructor for class halo.userinterface.gui.guitools.InputHelpDialog
Initializes the dialog frame
InvalidFlagException - Exception in halo.userinterface.cmdline.cmdexceptions
Exception that is called if a method is called with a flag that is not specified
InvalidFlagException() - Constructor for exception halo.userinterface.cmdline.cmdexceptions.InvalidFlagException
Creates a new exception
InvalidFlagException(String) - Constructor for exception halo.userinterface.cmdline.cmdexceptions.InvalidFlagException
Creates a new exception with the causing flag
InvalidMethodException - Exception in halo.userinterface.cmdline.cmdexceptions
Exception which is thrown when an invalid method is used
InvalidMethodException() - Constructor for exception halo.userinterface.cmdline.cmdexceptions.InvalidMethodException
Creates a new exception
InvalidMethodException(String) - Constructor for exception halo.userinterface.cmdline.cmdexceptions.InvalidMethodException
Creates a new exception
isCalls() - Method in class halo.userinterface.gui.GuiFilterData
Returns status of attributes in original file: present calls?
isCalls() - Method in class halo.userinterface.gui.session.Session
Returns status of attributes from original file: present calls?
isCancel() - Method in class halo.userinterface.gui.guitools.InputHelpDialog
Returns true if dialog was canceled
isCancel() - Method in class halo.userinterface.gui.guitools.LabelChooserDialog
Returns the cancel status of the dialog procedure
isCheckAbs() - Method in class halo.userinterface.gui.session.Session
Returns information on the checked status of the checkbox for the filtering method 'absence'
isCheckFilt() - Method in class halo.userinterface.gui.session.Session
Returns information on the checked status of the checkbox for filtering
isCheckHL() - Method in class halo.userinterface.gui.session.Session
Returns information on the checked status of the checkbox for half-life calculation
isCheckNorm() - Method in class halo.userinterface.gui.session.Session
Returns information on the checked status of the checkbox for normalization
isCheckPQS() - Method in class halo.userinterface.gui.session.Session
Returns information on the checked status of the checkbox for the filtering method 'pqs'
isCheckPQSMin() - Method in class halo.userinterface.gui.session.Session
Returns information on the checked status of the checkbox for the filtering method 'pqs min'
isCheckThresh() - Method in class halo.userinterface.gui.session.Session
Returns information on the checked status of the checkbox for the filtering method 'threshold'
isLineValid(String) - Static method in class halo.tools.Tools
Tests if a given line is composed of the letters a-z (case ignored), numbers or whitespace symbols like TAB
isLog() - Method in class halo.userinterface.gui.GuiFilterData
Returns scale of data (log or linear)
isMaxim() - Method in class halo.userinterface.gui.session.Session
Returns maximized status
isPlotQuality() - Method in class halo.userinterface.gui.session.Session
Returns status of quality plotting
isTurnReverseMapOff() - Static method in class halo.data.Mapping
Returns TRUE if reverse map is turned off
isUnequal() - Method in class halo.data.Data
Returns TRUE if unequal number of RNA measurements has been loaded.
isValid() - Static method in class halo.userinterface.cmdline.CmdFilterData
Checks whether all needed values are set
isValid() - Static method in class halo.userinterface.cmdline.CmdNormalization
checks whether all essential variables have been set
iterate() - Method in class halo.data.Mapping
Provides an iterator to iterate over the keys of the Mapping
iterateSpots(U) - Method in class halo.data.Mapping
Provides an iterator to iterate over the keys corresponding to a certain attribute

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