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SampleUseCase1
- Class in
halo.examples
First sample use case to demonstrate the handling of data from a given file.
SampleUseCase1()
- Constructor for class halo.examples.
SampleUseCase1
SampleUseCase2
- Class in
halo.examples
The third sample use case, which demonstrates the calculation and plotting of half-lives.
SampleUseCase2()
- Constructor for class halo.examples.
SampleUseCase2
SampleUseCase3
- Class in
halo.examples
The fourth sample use case, which demonstrates the sequence-based evaluation of the input data.
SampleUseCase3()
- Constructor for class halo.examples.
SampleUseCase3
saveData()
- Method in class halo.userinterface.gui.
GuiFilterData
Saves the Data object into a file
saveGraph(File)
- Method in class halo.userinterface.gui.graphhandler.
HistogramConstructor
Saves the graph as a JPEG picture
saveGraph(File)
- Method in class halo.userinterface.gui.graphhandler.
XYGraphConstructor
Saves the graph as a JPEG picture
saveHL()
- Method in class halo.userinterface.gui.
GuiHalfLife
Based on calculated half-lives, writes results into output file
saveHLWithAttributes(int, String, ArrayList<String>)
- Method in class halo.userinterface.gui.
GuiHalfLife
savePlotFile(File)
- Method in class halo.userinterface.gui.graphhandler.
HistogramConstructor
Saves the plotting information of the histogram
savePlotFile(File)
- Method in class halo.userinterface.gui.graphhandler.
XYGraphConstructor
Generates a plotting file with tab separations
savePlottingFileDialog()
- Method in class halo.userinterface.gui.
Gui
SEQUENCEFILE
- Static variable in class halo.examples.
SampleUseCase1
Session
- Class in
halo.userinterface.gui.session
Contains all information of a current session, as well as methods for saving and loading
Session(File)
- Constructor for class halo.userinterface.gui.session.
Session
Constructs a new session
Session()
- Constructor for class halo.userinterface.gui.session.
Session
Constructs a new session with a default file name
setAbsent(String)
- Method in class halo.data.
Data
Sets the name of the column (column label) which holds information on present/absent.
setAlpha(Alpha)
- Method in class halo.halflife.
HalfLife
Sets the Alpha object defining the method for calculation of alpha(t)
setAlpha(Alpha)
- Method in class halo.userinterface.gui.
GuiHalfLife
Sets the alpha object
setAlpha(String)
- Method in class halo.userinterface.gui.session.
Session
Sets the name of the used alpha function
setAttrDescr(String[])
- Method in class halo.data.
Data
Sets the description of all attributes.
setAttrDescr(String[])
- Method in class halo.userinterface.gui.session.
Session
Sets the descriptor for the attributes
setAttributeFiles(List<String>)
- Method in class halo.userinterface.gui.session.
Session
Sets the list of attribute files
setAttributeLabels(ArrayList<ArrayList<String>>)
- Method in class halo.userinterface.gui.session.
Session
setAttributes(ArrayList<Mapping<String, String>>)
- Method in class halo.data.
Data
Sets the attributes list for the data.
setAttributes(List<String>)
- Method in class halo.userinterface.gui.
GuiFilterData
Sets the list of attributes corresponding to the data
setAttributes(ArrayList<String>)
- Method in class halo.userinterface.gui.session.
Session
Sets the list of attribute labels
setAttributesInFile(boolean)
- Method in class halo.userinterface.gui.
GuiFilterData
Sets a variable that remembers if attributes were loaded from original file
setAttributesOut(List<String>)
- Method in class halo.userinterface.gui.
GuiFilterData
Sets the list of attributes for output
setC_l(double)
- Method in class halo.normalization.
CorrectionFactors
Sets the correction factor c_l
setC_lu(double)
- Method in class halo.normalization.
CorrectionFactors
Sets the correction factor c_lu
setC_u(double)
- Method in class halo.normalization.
CorrectionFactors
Sets the correction factor c_u
setCalls(boolean)
- Method in class halo.userinterface.gui.session.
Session
Sets status of attributes from original file
setCcl(double)
- Method in class halo.userinterface.gui.session.
Session
Sets the value of the parameter ccl
setCheckAbs(boolean)
- Method in class halo.userinterface.gui.session.
Session
Sets the value holding information on the checked status of the filtering method 'absence'
setCheckFilt(boolean)
- Method in class halo.userinterface.gui.session.
Session
Sets the value holding information on the checked status of the checkbox that expands the filtering menu
setCheckHL(boolean)
- Method in class halo.userinterface.gui.session.
Session
Sets the value holding information on the checked status of the checkbox that expands the half-life calculation
setCheckNorm(boolean)
- Method in class halo.userinterface.gui.session.
Session
Sets the value holding information on the checked status of the checkbox that expands the linear regression
setCheckPQS(boolean)
- Method in class halo.userinterface.gui.session.
Session
Sets the value holding information on the checked status of the filtering method 'pqs'
setCheckPQSMin(boolean)
- Method in class halo.userinterface.gui.session.
Session
Sets the value holding information on the checked status of the filtering method 'pqs min'
setCheckThresh(boolean)
- Method in class halo.userinterface.gui.session.
Session
Sets the value holding information on the checked status of the filtering method 'threshold'
setColor(Color)
- Method in class halo.userinterface.gui.graphhandler.
HistogramConstructor
setColumn(int)
- Method in class halo.userinterface.gui.session.
Session
Sets the column of the multiple fasta file header which holds the gene name
setColumnsNew(List<String>)
- Method in class halo.userinterface.gui.session.
Session
Sets the list of column labels for newly transcribed RNA, only those that are extracted
setColumnsPre(List<String>)
- Method in class halo.userinterface.gui.session.
Session
Sets the list of column labels for pre-existing RNA, only those that are extracted
setColumnsTotal(List<String>)
- Method in class halo.userinterface.gui.session.
Session
Sets the list of column labels for total RNA, only those that are extracted
setCombined(boolean)
- Method in class halo.userinterface.gui.
GuiFilterData
Defines whether single or combined filtering should be performed
setCorr(CorrectionFactors)
- Method in class halo.normalization.
Normalization
Sets the correction factors
setCorr(CorrectionFactors)
- Method in class halo.userinterface.gui.
GuiHalfLife
Sets the correction factors needed for half-life calculation
setCorrectionFactor(CorrectionFactors)
- Method in class halo.halflife.
HalfLife
Sets the set of correction factors
setCorrectionFactor(CorrectionFactors)
- Method in class halo.halflife.
HalfLife_New
setCorrectionFactor(CorrectionFactors)
- Method in class halo.halflife.
HalfLife_NewPre
setCorrectionFactor(CorrectionFactors)
- Method in class halo.halflife.
HalfLife_Pre
setCorrectionFactors(double, double)
- Method in class halo.halflife.
HalfLife
Sets the correction factors c_u and c_l
setCorrNewPre(HashMap<String, Double>)
- Method in class halo.data.
Data
Sets the correction bias values for the ratio newly transcribed/pre-existing.
setCorrNewTot(HashMap<String, Double>)
- Method in class halo.data.
Data
Sets the correction bias values for the ratio newly transcribed/total.
setCorrPreTot(HashMap<String, Double>)
- Method in class halo.data.
Data
Sets the correction bias values for the ratio pre-existing/total.
setData(Data)
- Method in class halo.userinterface.gui.
GuiHalfLife
Sets the data on which the half-life calculation is based
setData(Data)
- Method in class halo.userinterface.gui.
GuiNormal
Sets the data object for normalization
setData(Data)
- Method in class halo.userinterface.gui.session.
Session
Sets the data object needed for normalization
setDataFile(File)
- Method in class halo.userinterface.gui.session.
Session
Sets the file containing the data
setDataMethods(List<String>)
- Method in class halo.userinterface.gui.session.
Session
Sets the list of filtering methods
setDisplay(StringBuffer)
- Method in class halo.userinterface.gui.session.
Session
Sets the description of all used half-life calculation methods
setDisplayExit(boolean)
- Static method in class halo.userinterface.gui.session.
Config
Sets the information if exit dialog should be displayed
setDisplayHint(boolean)
- Static method in class halo.userinterface.gui.session.
Config
Sets the information if question mark dialog should be displayed
setFasta(String, int)
- Method in class halo.userinterface.gui.
GuiFilterData
Sets the file containing the sequences for the data, as well as the column defining where the gene name is found in the header of each sequence
setFasta(File)
- Method in class halo.userinterface.gui.session.
Session
Sets the file which contains the sequences for the data
setFile(File)
- Method in class halo.userinterface.gui.
GuiFilterData
Sets the file containing the initial data
setFile(File)
- Method in class halo.userinterface.gui.session.
Session
Sets the file into which the session will be saved
setFileName(String)
- Method in class halo.data.biascorrection.
RCorrelationCoefficient
Sets the name of the script file
setFileName(String)
- Method in class halo.data.biascorrection.
RLoessRegression
Sets the file name of the script file
setFilename(String)
- Method in class halo.data.
Data
Sets the name of the file holding the data information.
setFirst(boolean)
- Method in class halo.userinterface.gui.
GuiFilterData
Sets status if data is loaded for the first time
setGeneLabel(String)
- Method in class halo.userinterface.gui.session.
Session
Sets the gene name label
setGeneName(String)
- Method in class halo.data.
Data
Sets the name of the column which holds information on the gene name.
setGenename(String)
- Method in class halo.userinterface.gui.
GuiFilterData
Sets the name of the gene name attribute
setGuiData(GuiFilterData)
- Method in class halo.userinterface.gui.session.
Session
Sets the interface between GUI and data handling
setGuiHL(GuiHalfLife)
- Method in class halo.userinterface.gui.session.
Session
Sets the interface between GUI and half-life calculation
setGuiNorm(GuiNormal)
- Method in class halo.userinterface.gui.session.
Session
Sets the interface between GUI and normalization
setHlMethods(List<String>)
- Method in class halo.userinterface.gui.session.
Session
Sets the list of descriptions of half-life calculation methods
setHwz(double[])
- Method in class halo.halflife.
HalfLife
Sets the half-life values
setInputFile(File)
- Method in class halo.data.biascorrection.
CorrelationCoefficient
Sets the input file that holds the data
setInputFile(File)
- Method in class halo.data.biascorrection.
LoessRegression
Sets the file that contains the data
setLabelingTime(double)
- Method in class halo.userinterface.gui.session.
Session
Sets the constant labeling time
setLabels(ArrayList<String>)
- Method in class halo.userinterface.gui.session.
Session
Sets the list of all labels from the data file
setLabelsNew(List<String>)
- Method in class halo.userinterface.gui.
GuiFilterData
Sets the column labels for newly transcribed RNA that will be read in
setLabelsPre(List<String>)
- Method in class halo.userinterface.gui.
GuiFilterData
Sets the column labels for pre-existing RNA that will be read in
setLabelsTot(List<String>)
- Method in class halo.userinterface.gui.
GuiFilterData
Sets the column labels for total RNA that will be read in
setLog(boolean)
- Method in class halo.userinterface.gui.
GuiFilterData
Sets the scale; true for log scale, false for linear
setLog(boolean)
- Method in class halo.userinterface.gui.session.
Session
Sets scale of data (log or linear)
setMap(Mapping<String, Integer>)
- Method in class halo.data.
Data
Sets the mapping corresponding to the whole data and filtered values.
setMax(double)
- Method in class halo.userinterface.gui.
GuiHalfLife
Sets the maximal value for half-life values
setMaxim(int)
- Method in class halo.userinterface.gui.session.
Session
Sets the attribute containing information if the window is maximized or not
setMaximum(double)
- Method in class halo.data.
Data
Sets the maximum RNA value
setMaximumHalfLife(double)
- Static method in class halo.halflife.
HalfLife
Sets the maximum half-life value to be used
setMethod(String)
- Method in class halo.data.biascorrection.
RCorrelationCoefficient
Sets the method for the calculation of the correlation coefficient
setMethod(int)
- Method in class halo.data.
Data
Sets the method used for calculating the average ratios over all replicates.
setMethod(String)
- Method in class halo.userinterface.gui.
GuiNormal
Sets the name of the normalization method
setMethods(List<String>)
- Method in class halo.userinterface.gui.
GuiFilterData
Sets the list of filtering methods
setMethods(List<String>)
- Method in class halo.userinterface.gui.
GuiHalfLife
Sets the list of method descriptions for calculation
setMin(double)
- Method in class halo.userinterface.gui.
GuiHalfLife
Sets the minimum value for half-life values
setMinimum(double)
- Method in class halo.data.
Data
Sets the minimum RNA value
setMinimumHalfLife(double)
- Static method in class halo.halflife.
HalfLife
Sets the minimal half-life value to be used
setNewMap(Mapping<String, Integer>)
- Method in class halo.halflife.
HalfLife
Sets the mapping corresponding to the ratio values
setNewOut(List<String>)
- Method in class halo.userinterface.gui.
GuiFilterData
Sets the column labels for newly transcribed RNA that will be written into the output
setNorm(Normalization)
- Method in class halo.userinterface.gui.
GuiFilterData
Sets the normalization object needed for evaluation
setNormMethod(String)
- Method in class halo.userinterface.gui.session.
Session
Sets the list of methods for normalization
setOriginalAtts(List<String>)
- Method in class halo.userinterface.gui.
GuiFilterData
Sets the attributes from the data file
setOriginalLabelsCalls(List<String>)
- Method in class halo.userinterface.gui.session.
Session
Sets the list of attributes from the original file (present calls)
setOriginalLabelsOther(List<String>)
- Method in class halo.userinterface.gui.session.
Session
Sets the list of attributes from the original file (no present calls)
setOutput(File)
- Method in class halo.userinterface.gui.
GuiFilterData
Sets the file in which the filtered data will be written
setOutput(String, int)
- Method in class halo.userinterface.gui.
GuiHalfLife
Sets all necessary variables for defining the output
setPath(String)
- Method in class halo.data.biascorrection.
RMethods
Define the installation path of R
setPathR(String)
- Method in class halo.userinterface.gui.session.
Session
Sets the constant path to R
setPathToR(String)
- Static method in class halo.userinterface.gui.session.
Config
Sets the path to the bin folder of the R installation
setPlotQuality(boolean)
- Method in class halo.userinterface.gui.session.
Session
Sets status of quality plotting
setPoints(boolean[])
- Method in class halo.userinterface.gui.graphhandler.
XYGraphConstructor
Sets the point definitions
setPosX(int)
- Method in class halo.userinterface.gui.session.
Session
Sets the x position of the window
setPosY(int)
- Method in class halo.userinterface.gui.session.
Session
Sets the y position of the window
setPqs(double[])
- Method in class halo.data.
Data
Sets the probe set quality scores.
setPQSName(String)
- Method in class halo.userinterface.gui.
GuiFilterData
Sets the name of the file in which the quality scores will be written
setPqsPlot(boolean)
- Method in class halo.userinterface.gui.
GuiFilterData
Sets the pqs-plot variable
setPreOut(List<String>)
- Method in class halo.userinterface.gui.
GuiFilterData
Sets the column labels for pre-existing RNA that will be written into the output
setRatioMethod(int)
- Method in class halo.userinterface.gui.
GuiHalfLife
Changes the method used for ratio calculation
setRatioMethod(int)
- Method in class halo.userinterface.gui.
GuiNormal
Changes the method used for ratio calculation
setRatioMethod(int)
- Method in class halo.userinterface.gui.session.
Session
Sets the ratio calculation method
setReplicate(int)
- Method in class halo.data.
Data
Sets the replicate used for ratio calculations, if method is restricting of ratios to one replicate.
setReplicate(int)
- Method in class halo.normalization.
Normalization
Sets the replicate for calculation
setReplicate(int)
- Method in class halo.userinterface.gui.
GuiNormal
Sets the replicate for normalization
setReplicate(int)
- Method in class halo.userinterface.gui.session.
Session
Sets a constant replicate
setReplicates(List<Integer>)
- Method in class halo.userinterface.gui.
GuiHalfLife
Sets the numbers of the replicates for the half-life calculations
setReplicates(List<Integer>)
- Method in class halo.userinterface.gui.session.
Session
Sets the (column) number of the used replicate
setSessionFile(String)
- Static method in class halo.userinterface.gui.session.
Config
Sets the path of the session file
setSpotid(String)
- Method in class halo.data.
Data
Sets the name of the column with probeset ids.
setSpotid(String)
- Method in class halo.userinterface.gui.
GuiFilterData
Sets the name of the column with probe-set-ids
setTimes(List<Double>)
- Method in class halo.userinterface.gui.
GuiHalfLife
Sets the list of time points for calculation, order corresponding to the list of methods
setTimes(List<Double>)
- Method in class halo.userinterface.gui.session.
Session
Sets the list of time points for half-life calculation
setTotOut(List<String>)
- Method in class halo.userinterface.gui.
GuiFilterData
Sets the column labels for total RNA that will be written into the output
setTurnReverseMapOff(boolean)
- Static method in class halo.data.
Mapping
Allows user to turn the reverse map off for attributes like present/absent calls with large numbers of equal attributes
setTurnReverseMapOff(boolean)
- Method in class halo.userinterface.gui.
GuiFilterData
Should be set true for present calls
setUnequal(boolean)
- Method in class halo.data.
Data
Set the value of the unequal variable, meaning if there is an unequal number of measurements (new, pre, total).
setUserbrowser(String)
- Static method in class halo.userinterface.gui.session.
Config
Sets the user browser
shift(String[])
- Static method in class halo.userinterface.cmdline.
CommandLine
Shifts the content of a given String array one position to the left, thereby erasing the first element
showBrowser(URI, Frame)
- Static method in class halo.userinterface.gui.guitools.
GuiTools
Opens a given URI in a user defined browser
SPEARMAN
- Static variable in class halo.data.biascorrection.
RCorrelationCoefficient
split(String[])
- Static method in class halo.userinterface.cmdline.
CmdNormalization
Splits the options array into one array that provides input for the data manipulation and one array that provides needed input for calculation of normalization
STANDARD
- Static variable in class halo.userinterface.cmdline.
CmdNormalization
STANDARD
- Static variable in class halo.userinterface.gui.
GuiNormal
startRScript(String)
- Method in class halo.data.biascorrection.
RMethods
Start to write the R script
store()
- Method in class halo.userinterface.gui.session.
Session
Stores the session in the previously defined file
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