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A

AboutDialog - Class in halo.userinterface.gui.guitools
Displays a dialog with information about HALO
AboutDialog(Frame) - Constructor for class halo.userinterface.gui.guitools.AboutDialog
 
accept(File) - Method in class halo.userinterface.gui.guitools.JPEGFilter
Tests if a given file is accepted
accept(File) - Method in class halo.userinterface.gui.guitools.TxtFilter
 
addAttr(File, ArrayList<String>) - Method in class halo.userinterface.gui.GuiFilterData
Extracts a new attribute from a given file and adds it to the data
addAttributes(String) - Method in class halo.data.Data
Reads in every attribute from a given file.
addAttributes(String, ArrayList<String>) - Method in class halo.data.Data
Reads in regular attributes from a file.
addAttributes(String, ArrayList<String>, boolean) - Method in class halo.data.Data
Reads in a file containing several columns, of which one contains the spotID, the others contain attributes.
addAttributesList(ArrayList<Mapping<String, String>>, String[]) - Method in class halo.userinterface.gui.GuiFilterData
Adds a list of attributes to the data, as well as the corresponding descriptors
addData(double, double) - Method in class halo.userinterface.gui.graphhandler.XYGraphConstructor
Adds one single numerical pair to the graph, but only if there is only one series of data; this method should be used after 'addEmptySeries' to ensure no messing up of data that does not belong together
addData(double, ArrayList<Double>) - Method in class halo.userinterface.gui.graphhandler.XYGraphConstructor
Adds a number of numerical (x,y) pairs to the graph (scatterplot) , but only if the number is the same as the number of existing series; this method should be used after 'addEmptySeries' to ensure no messing up of data that does not belong together
addEmptySeries(ArrayList<String>) - Method in class halo.userinterface.gui.graphhandler.XYGraphConstructor
Creates a number of empty series and adds them to those yet existing
addEmptySeries(String) - Method in class halo.userinterface.gui.graphhandler.XYGraphConstructor
Creates one empty series and adds them to the existing ones
addEnding(String) - Method in class halo.userinterface.gui.guitools.JPEGFilter
Adds an accepted ending to the list
addFasta(File, int) - Method in class halo.userinterface.gui.GuiFilterData
Adds the necessary information for the multiple fasta file; its location and the column containing the gene name
addHL(String, double, int) - Method in class halo.userinterface.gui.GuiHalfLife
Add a half-life object to the current list, also add corresponding time
addLineToScript(String) - Method in class halo.data.biascorrection.RMethods
Write one line into the R script
addMap(T, U) - Method in class halo.data.Mapping
Add the values to the internal map as well as to the map containing the inverted values (attribute --> spotID)
addMethod(String, String) - Method in class halo.userinterface.gui.GuiFilterData
Adds a filtering method and a corresponding value, e.g. a threshold
addOriginalAttr(ArrayList<String>, boolean) - Method in class halo.userinterface.gui.GuiFilterData
 
addPresenceCalls(String, ArrayList<String>) - Method in class halo.data.Data
Reads in attributes from a file.
addSeries(String, double[], int, double, double) - Method in class halo.userinterface.gui.graphhandler.HistogramConstructor
Adds a complete data series to the graph
addSeries(ArrayList<Tuple<Double, Double>>, String) - Method in class halo.userinterface.gui.graphhandler.XYGraphConstructor
Adds a list of numerical pairs to the graph
addValue(double) - Method in class halo.userinterface.gui.graphhandler.HistogramConstructor
Adds a new value to the set of values
addValues(double[]) - Method in class halo.userinterface.gui.graphhandler.HistogramConstructor
Adds all values in an array to the set of values
alignLabel(String, int, FontMetrics) - Static method in class halo.userinterface.gui.guitools.GuiTools
Formats a text for a dialog window
Alpha - Interface in halo.halflife.alpha
Contains the function alpha used for half life calculation
alpha(double) - Method in interface halo.halflife.alpha.Alpha
Function that calculates alpha for a given time point t
alpha(double) - Method in class halo.halflife.alpha.AlphaCellDivision
The function that calculates alpha according to the cell division model function
alpha(double) - Method in class halo.halflife.alpha.AlphaConstant
Default function for alpha
ALPHACELLDIV - Static variable in class halo.userinterface.gui.session.Session
 
AlphaCellDivision - Class in halo.halflife.alpha
Provides an alpha calculation method for the modeling of cell division
AlphaCellDivision(double) - Constructor for class halo.halflife.alpha.AlphaCellDivision
Constructor for an alpha object for modeling of cell division
AlphaConstant - Class in halo.halflife.alpha
Contains the function alpha and its default value extendable for definition of new alpha functions
AlphaConstant() - Constructor for class halo.halflife.alpha.AlphaConstant
Constructor for a regular alpha object, returning 1 always
ALPHACONSTANT - Static variable in class halo.userinterface.gui.session.Session
 
AVERAGEFIRST - Static variable in class halo.data.Data
 

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