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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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