A B C D E F G H I J K L M N P R S T U V W X

C

calcHL() - Method in class halo.userinterface.gui.GuiHalfLife
Use set variables and create HalfLife objects for every method, calculate half-lives
calcHLonMedian(List<CorrectionFactors>) - Method in class halo.userinterface.gui.GuiHalfLife
Calculates the half-life values based on a list of correction factors which correspond to the list of half-lives
calcNormalization() - Method in class halo.userinterface.gui.GuiNormal
Creates Normalization object and performs normalization
calculateAverageFirst(double[][], double[][], HashMap<String, Double>) - Method in class halo.data.Data
Calculates the average values from all replicates for the linear regression through calculating the ratio of the averages (AVERAGEFIRST method).
calculateCorrectionFactors(double, double) - Method in class halo.halflife.HalfLife
Calculation of correction factors based on a median
calculateCorrectionFactors(double, double) - Method in class halo.halflife.HalfLife_New
 
calculateCorrectionFactors(double, double) - Method in class halo.halflife.HalfLife_NewPre
 
calculateCorrectionFactors(double, double) - Method in class halo.halflife.HalfLife_Pre
 
calculateCorrectionFactors() - Method in class halo.normalization.LinearRegression
 
calculateCorrectionFactors() - Method in class halo.normalization.Normalization
calculates correction factors via normalization methods
calculateCorrectionFactors(int) - Method in class halo.normalization.Normalization
Calculates the correction factors for a certain replicate
calculateCorrelationCoefficient() - Method in class halo.data.biascorrection.CorrelationCoefficient
Abstract method for the calculation of the correlation coefficient for the data
calculateCorrelationCoefficient() - Method in class halo.data.biascorrection.RCorrelationCoefficient
Start the calculation of the correlation coefficient
calculateHalfLives(double) - Method in class halo.halflife.HalfLife
Calculation of half-lives
calculateHalfLives(double) - Method in class halo.halflife.HalfLife_New
 
calculateHalfLives(double) - Method in class halo.halflife.HalfLife_NewPre
 
calculateHalfLives(double) - Method in class halo.halflife.HalfLife_Pre
 
calculateLoessRegression() - Method in class halo.data.biascorrection.LoessRegression
Abstract method for the calculation of the fitted values for correction of bias
calculateLoessRegression() - Method in class halo.data.biascorrection.RLoessRegression
Starts the calculation of the fitted values with R
calculateMappingForAttributes(String[][], String[]) - Method in class halo.data.Data
Transcribes the attributes into a mapping id -> attribute.
calculateMedian() - Method in class halo.userinterface.gui.GuiHalfLife
Calculate the median for a set of half-lives
calculateMedianForHalfLives(double, Data) - Static method in class halo.tools.Tools
Calculates the average median over two available half-life calculation methods
calculateNewMapping() - Method in class halo.data.Data
Calculates the Mapping corresponding to the ratio.
calculateQualityControl(Data, boolean) - Method in class halo.normalization.Normalization
Calculates the array containing the quality control values; these are calculated as distance from the normalization line
calculateRatio(double[][], double[][], HashMap<String, Double>, int) - Method in class halo.data.Data
Calculates filtered Ratio of a set of RNA values (e.g. newly transcribed RNA) to a second set of values (e.g. total RNA) based on the specified method to calculate the average of multiple replicates.
calculateRatio(double[][], double[][], HashMap<String, Double>) - Method in class halo.data.Data
Calculates the ratios for an average over a set of replicates.
calculateRatioFirst(double[][]) - Method in class halo.data.Data
calculates the average values from all replicates for the linear regression.
changeMap(T, U) - Method in class halo.data.Mapping
Change the attribute of a specific spotID
checkForGenes(Data) - Static method in class halo.data.Filter
Checks if the data object has the gene name attribute loaded and can be used for PQS filtering
clearHL() - Method in class halo.userinterface.gui.GuiHalfLife
Resets everything that has been used for half-life calculation of previous half-life list
close() - Method in class halo.userinterface.gui.guitools.LabelChooserDialog
Hides the dialog window
CmdFilterData - Class in halo.userinterface.cmdline
Serves as interface between Data manipulation tools and command line input
CmdFilterData() - Constructor for class halo.userinterface.cmdline.CmdFilterData
 
CmdHalfLife - Class in halo.userinterface.cmdline
Serves as interface between command line input and calculation of half-lives
CmdHalfLife() - Constructor for class halo.userinterface.cmdline.CmdHalfLife
 
CmdNormalization - Class in halo.userinterface.cmdline
Serves as interface between command line input and tools for calculation of linear regression
CmdNormalization() - Constructor for class halo.userinterface.cmdline.CmdNormalization
 
CommandLine - Class in halo.userinterface.cmdline
Class which forwards information from command line input to further classes which serve as interface between command line and tools for calculation
CommandLine() - Constructor for class halo.userinterface.cmdline.CommandLine
 
compareTo(Object) - Method in class halo.tools.Tuple
 
Config - Class in halo.userinterface.gui.session
Provides a set of final parameters describing paths and file names and saves user decisions for the display of certain dialogs
Config() - Constructor for class halo.userinterface.gui.session.Config
 
CONFIGDIR - Static variable in class halo.userinterface.gui.session.Config
 
CONFIGFILE - Static variable in class halo.userinterface.gui.session.Config
 
CONFIGPATH - Static variable in class halo.userinterface.gui.session.Config
 
containsAttribute(U) - Method in class halo.data.Mapping
Returns true if the given attribute exists in the Mapping
containsSpot(T) - Method in class halo.data.Mapping
Returns true if the given key exists in the Mapping
copyMap() - Method in class halo.data.Data
Copies the content of the Mapping object.
CorrectionFactors - Class in halo.normalization
Class for managing the correction factors needed for half-life calculation
CorrectionFactors() - Constructor for class halo.normalization.CorrectionFactors
Constructor setting the factors to the default value UNDEF = -1
CorrectionFactors(double, double) - Constructor for class halo.normalization.CorrectionFactors
Constructor setting only the factors c_l and c_u
CorrectionFactors(double) - Constructor for class halo.normalization.CorrectionFactors
Constructor setting only the factor c_lu
CorrectionFactors(double, double, double) - Constructor for class halo.normalization.CorrectionFactors
Constructor setting all three correction factors
CorrelationCoefficient - Class in halo.data.biascorrection
Abstract class for the calculation of the correlation coefficient of a data set
CorrelationCoefficient() - Constructor for class halo.data.biascorrection.CorrelationCoefficient
 
CORRELATIONCOEFFICIENT - Static variable in class halo.userinterface.gui.session.Config
 

A B C D E F G H I J K L M N P R S T U V W X