Uses of Class
halo.data.Data

Packages that use Data
halo.data Provides for the extraction, filtering, handling and saving of expression data. 
halo.examples Provides easy-to-understand examples for the usage of HALO. 
halo.halflife Provides for the calculation and handling of half-lives. 
halo.normalization Provides for the calculation and handling of normalization. 
halo.tools Provides a set of tools applicable for several uses. 
halo.userinterface.cmdline Provides for the handling of user input and starting of corresponding calculations. 
halo.userinterface.gui Provides for the generation and handling of a graphical user interface, as well as the starting of corresponding calculations according to user input. 
halo.userinterface.gui.graphhandler Provides for generation of plots and histograms. 
halo.userinterface.gui.session Provides for the handling, saving and loading of sessions and configuration information. 
 

Uses of Data in halo.data
 

Methods in halo.data that return Data
static Data Filter.filter(Data data, double threshold)
          removes all experiments where at least one of the values is beneath a certain threshold Commandline option -f threshold='value'
static Data Filter.filterAbsent(Data data, java.util.ArrayList<java.lang.String> relevantColumns, java.lang.String call, int threshold)
          Removes values that are defined as 'absent' in the attribute list Commandline option -f present='label1,label2,...
static Data Filter.filterCorrectionBias(Data data, java.util.HashMap<java.lang.String,java.lang.Double> corr)
          Filters the data according to given values for bias correction in such a way that only those probeset ids are kept that have corresponding correction values
static Data Filter.filterPQS(Data data, Normalization l, boolean histogram)
          Please note that this method can only be used after normalization!
static Data Filter.filterPQS(Data data, Normalization l, double threshold, boolean histogram)
          Please note that this method can only be used after normalization!
static Data Filter.filterPQS(Data data, Normalization l, int replicate, boolean histogram)
          Please note that this method can only be used after normalization!
static Data Filter.transferAllValues(Data oldData, Data newData)
          Transfers all values that are not directly used in filtering from the old data object to the new data object
 

Methods in halo.data with parameters of type Data
static boolean Filter.checkForGenes(Data data)
          Checks if the data object has the gene name attribute loaded and can be used for PQS filtering
static Data Filter.filter(Data data, double threshold)
          removes all experiments where at least one of the values is beneath a certain threshold Commandline option -f threshold='value'
static Data Filter.filterAbsent(Data data, java.util.ArrayList<java.lang.String> relevantColumns, java.lang.String call, int threshold)
          Removes values that are defined as 'absent' in the attribute list Commandline option -f present='label1,label2,...
static Data Filter.filterCorrectionBias(Data data, java.util.HashMap<java.lang.String,java.lang.Double> corr)
          Filters the data according to given values for bias correction in such a way that only those probeset ids are kept that have corresponding correction values
static Data Filter.filterPQS(Data data, Normalization l, boolean histogram)
          Please note that this method can only be used after normalization!
static Data Filter.filterPQS(Data data, Normalization l, double threshold, boolean histogram)
          Please note that this method can only be used after normalization!
static Data Filter.filterPQS(Data data, Normalization l, int replicate, boolean histogram)
          Please note that this method can only be used after normalization!
static Data Filter.transferAllValues(Data oldData, Data newData)
          Transfers all values that are not directly used in filtering from the old data object to the new data object
 

Uses of Data in halo.examples
 

Methods in halo.examples that return Data
static Data SampleUseCase1.run()
          Starts the loading, filtering and printing of data
 

Methods in halo.examples with parameters of type Data
static double SampleUseCase2.median(Data data, java.util.ArrayList<HalfLife> medMethods, double time)
          Calculates the median half-life for a set of methods and a given time
 

Uses of Data in halo.halflife
 

Methods in halo.halflife that return Data
 Data HalfLife.getData()
          Returns the data object holding the original data
 

Methods in halo.halflife with parameters of type Data
 void HalfLife_New.initialize(Data data)
           
 void HalfLife_NewPre.initialize(Data data)
           
abstract  void HalfLife.initialize(Data data)
          initializes the HalfLife object & extracts the needed values of the Data object
 void HalfLife_Pre.initialize(Data data)
           
 void HalfLife_New.initialize(Data data, int replicate)
           
 void HalfLife_NewPre.initialize(Data data, int replicate)
           
abstract  void HalfLife.initialize(Data data, int replicate)
          initializes the HalfLife object for a specific replicate of the data
 void HalfLife_Pre.initialize(Data data, int replicate)
           
 

Uses of Data in halo.normalization
 

Methods in halo.normalization with parameters of type Data
 double[] Normalization.calculateQualityControl(Data data, boolean histogram)
          Calculates the array containing the quality control values; these are calculated as distance from the normalization line
 

Constructors in halo.normalization with parameters of type Data
LinearRegression(Data data)
          Constructor for simple linear regression object
 

Uses of Data in halo.tools
 

Methods in halo.tools with parameters of type Data
static double Tools.calculateMedianForHalfLives(double time, Data data)
          Calculates the average median over two available half-life calculation methods
 

Uses of Data in halo.userinterface.cmdline
 

Methods in halo.userinterface.cmdline that return Data
static Data CmdNormalization.getData(java.lang.String[] input)
          Uses the complete options array to split it and forward the necessary information to the interface for data manipulation
static Data CmdFilterData.prepareData(java.lang.String[] input)
          Creates a data object from the information given as options array
 

Methods in halo.userinterface.cmdline with parameters of type Data
static Normalization CmdFilterData.performNormalization(Data data)
          Performs normalization on a given Data object with the previously specified method
static CorrectionFactors CmdNormalization.prepareNormalization(Data data)
          Contains all the methods for calculation of normalization
 

Uses of Data in halo.userinterface.gui
 

Methods in halo.userinterface.gui that return Data
 Data GuiFilterData.getData()
          Returns the complete Data object
 

Methods in halo.userinterface.gui with parameters of type Data
 void GuiNormal.setData(Data data)
          Sets the data object for normalization
 void GuiHalfLife.setData(Data data)
          Sets the data on which the half-life calculation is based
 

Uses of Data in halo.userinterface.gui.graphhandler
 

Methods in halo.userinterface.gui.graphhandler with parameters of type Data
static XYGraphConstructor GraphHandler.plotNormalization(Normalization norm, Data data)
          Generates the plot for normalization
 

Uses of Data in halo.userinterface.gui.session
 

Methods in halo.userinterface.gui.session that return Data
 Data Session.getData()
          Returns the data object
 

Methods in halo.userinterface.gui.session with parameters of type Data
 void Session.setData(Data data)
          Sets the data object needed for normalization