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

G

GENEDEFAULT - Static variable in class halo.data.Data
 
generateConfigFile(boolean, boolean, String) - Static method in class halo.userinterface.gui.session.Config
Generates a file that saves information about the display of the information dialog on program start, exit dialog on program exit, and path of the session file
generateConfigFile() - Static method in class halo.userinterface.gui.session.Config
Generates a file that saves information about the display of the information dialog on program start, exit dialog on program exit, and path of the session file based on previously loaded values
generateGraph() - Method in class halo.userinterface.gui.graphhandler.HistogramConstructor
Generates a graph from the given series
generateGraph() - Method in class halo.userinterface.gui.graphhandler.XYGraphConstructor
Generates a graph from the loaded data and displays it
generateHistogram(double[], double) - Method in class halo.normalization.Normalization
Uses the PQS data and generates a histogram from it
generateHL() - Method in class halo.userinterface.gui.GuiHalfLife
Generate empty HalfLife objects according to the given methods, without calculating the half-lives
getAbsent() - Method in class halo.data.Data
Returns the call used for present/absent filtering.
getAbsentLabel() - Method in class halo.data.Data
Returns the name of the column with present/absent calls.
getAcceptedEndings() - Method in class halo.userinterface.gui.guitools.JPEGFilter
Returns the list of accepted endings
getAlpha() - Method in class halo.halflife.HalfLife
Returns the alpha object defining the calculation method of alpha
getAlpha() - Method in class halo.normalization.Normalization
Returns the factor alpha from normalization
getAlpha() - Method in class halo.userinterface.gui.GuiHalfLife
Returns the alpha function of the first half-life object, based on the assumption that all objects use the same alpha
getAlpha() - Method in class halo.userinterface.gui.session.Session
Returns the name of the used alpha function
getAttrDescr() - Method in class halo.data.Data
Returns the description of the attributes.
getAttrDescr() - Method in class halo.userinterface.gui.GuiFilterData
Returns the descriptors for the attribute list
getAttrDescr() - Method in class halo.userinterface.gui.session.Session
Returns the names of the attributes for the data
getAttribute(T) - Method in class halo.data.Mapping
Retrieves the attribute for one given key
getAttributeFiles() - Method in class halo.userinterface.gui.session.Session
Returns the list of attribute file names
getAttributeLabels() - Method in class halo.userinterface.gui.session.Session
Returns the list of attribute label names
getAttributes() - Method in class halo.data.Data
Returns the attribute lists.
getAttributes() - Method in class halo.userinterface.gui.session.Session
Returns the list of all attributes
getAttributesList() - Method in class halo.userinterface.gui.GuiFilterData
Returns the list of attributes for the data
getAvgL() - Method in class halo.userinterface.gui.GuiFilterData
Returns the average log(e'/n')
getAvgLo() - Method in class halo.data.Data
Returns the average log(e'/n').
getAvgU() - Method in class halo.userinterface.gui.GuiFilterData
Returns the average number of uracils
getAvgUr() - Method in class halo.data.Data
Returns the average number of Uracil.
getBeta() - Method in class halo.normalization.Normalization
Returns the factor beta from normalization
getC_l() - Method in class halo.halflife.HalfLife
Returns the correction factor c_l
getC_l() - Method in class halo.normalization.CorrectionFactors
Returns the correction factor c_l
getC_lu() - Method in class halo.normalization.CorrectionFactors
Returns the correction factor c_lu
getC_u() - Method in class halo.halflife.HalfLife
Returns the correction factor c_u
getC_u() - Method in class halo.normalization.CorrectionFactors
Returns the correction factor c_u
getCcl() - Method in class halo.halflife.alpha.AlphaCellDivision
Returns the parameter ccl
getCcl() - Method in class halo.userinterface.gui.session.Session
Returns the value of the parameter ccl
getCF() - Method in class halo.userinterface.gui.GuiNormal
Returns the correction factors
getCFonMedian(double) - Method in class halo.userinterface.gui.GuiHalfLife
Calculates the median for each HalfLife object and the correction factors based on this median
getColumn() - Method in class halo.userinterface.gui.GuiFilterData
Returns the column of the fasta header that keeps the gene name
getColumnLabels(File) - Static method in class halo.tools.Tools
Reads the header/description line of a given file and provides all column labels (columns separated by tabulator) as a list
getColumnsNew() - Method in class halo.userinterface.gui.session.Session
Returns the list of column labels for newly transcribed RNA, only the extracted ones
getColumnsPre() - Method in class halo.userinterface.gui.session.Session
Returns the list of column labels for pre-existing RNA, only the extracted ones
getColumnsTotal() - Method in class halo.userinterface.gui.session.Session
Returns the list of column labels for total RNA, only the extracted ones
getCorr() - Method in class halo.normalization.Normalization
Returns the correction factors
getCorrNewPre() - Method in class halo.data.Data
Returns the correction bias values for the ratio newly transcribed/pre-existing.
getCorrNewTot() - Method in class halo.data.Data
Returns the correction bias values for the ratio newly transcribed/total.
getCorrPreTot() - Method in class halo.data.Data
Returns the correction bias values for the ratio pre-existing/total.
getDat() - Method in class halo.data.Data
Returns the evaluated normalized data.
getData() - Method in class halo.halflife.HalfLife
Returns the data object holding the original data
getData(String[]) - Static method in class halo.userinterface.cmdline.CmdNormalization
Uses the complete options array to split it and forward the necessary information to the interface for data manipulation
getData() - Method in class halo.userinterface.gui.GuiFilterData
Returns the complete Data object
getData() - Method in class halo.userinterface.gui.session.Session
Returns the data object
getDataFile() - Method in class halo.userinterface.gui.session.Session
Returns the file from which the data was extracted
getDataMethods() - Method in class halo.userinterface.gui.session.Session
Returns the list of filtering methods
getDescription() - Method in class halo.userinterface.gui.guitools.JPEGFilter
Returns the description of the filter
getDescription() - Method in class halo.userinterface.gui.guitools.TxtFilter
 
getDisplay() - Method in class halo.userinterface.gui.session.Session
Returns the description of half-life calculation methods and time points
getDisplayExit() - Static method in class halo.userinterface.gui.session.Config
Returns true if exit dialog should be displayed
getDisplayHint() - Static method in class halo.userinterface.gui.session.Config
Returns true if question mark dialog should be displayed
getFasta() - Method in class halo.userinterface.gui.GuiFilterData
Returns the file containing the sequences for the data
getFilename() - Method in class halo.data.Data
Returns the name of the file containing the data.
getFirst() - Method in class halo.tools.Tuple
Returns the first value for the tuple
getFlag() - Method in exception halo.userinterface.cmdline.cmdexceptions.InvalidFlagException
Returns the causing flag
getGeneLabel() - Method in class halo.userinterface.gui.session.Session
Returns the saved gene label
getGeneName() - Method in class halo.data.Data
Returns the name of the column with gene names.
getGenename() - Method in class halo.userinterface.gui.GuiFilterData
Returns the name of the column with gene names
getGuiData() - Method in class halo.userinterface.gui.session.Session
Returns the interface connecting GUI and filtering of the data
getGuiHL() - Method in class halo.userinterface.gui.session.Session
Returns the interface connecting GUI and half-life calculation
getGuiNorm() - Method in class halo.userinterface.gui.session.Session
Returns the interface connecting GUI and linear regression
getHL() - Method in class halo.userinterface.gui.GuiHalfLife
Returns the list of half-life objects calculated
getHlMethods() - Method in class halo.userinterface.gui.session.Session
Returns the list of methods used for half-life calculation
getHwz() - Method in class halo.halflife.HalfLife
Returns the half-life values
getInputText() - Method in class halo.userinterface.gui.guitools.InputHelpDialog
Returns the user input
getLabelingTime() - Method in class halo.userinterface.gui.session.Session
Returns the labeling time
getLabels() - Method in class halo.userinterface.gui.session.Session
Returns all the labels available in the data file
getList() - Method in class halo.userinterface.gui.guitools.LabelChooserDialog
Returns the list of components
getMap() - Method in class halo.data.Data
Returns the map corresponding to the data.
getMax() - Method in class halo.halflife.HalfLife
Returns the highest present half-life value
getMaximum() - Method in class halo.data.Data
Returns the maximal expression value present in the data
getMaximumHalfLife() - Static method in class halo.halflife.HalfLife
Returns the set maximum half-life
getMD() - Method in class halo.userinterface.gui.GuiHalfLife
Returns the last calculated median
getMethod() - Method in class halo.data.Data
Returns the number of the method used for ratio calculation.
getMethods() - Method in class halo.userinterface.gui.GuiFilterData
Returns the list of filtering methods
getMethods() - Method in class halo.userinterface.gui.GuiHalfLife
Returns the list of method descriptions used for half-life calculation
getMinimum() - Method in class halo.data.Data
Returns the minimal expression value present in the data
getMinimumHalfLife() - Static method in class halo.halflife.HalfLife
Returns the set minimum half-life
getName() - Method in class halo.halflife.HalfLife
Returns the name of this method
getNewDescr() - Method in class halo.data.Data
Returns the description = column labels of newly transcribed RNA.
getNewMapping() - Method in class halo.halflife.HalfLife
Returns the mapping corresponding to ratios/half-lives
getNewRNA() - Method in class halo.data.Data
Returns all the values for newly transcribed RNA.
getNormalization() - Method in class halo.userinterface.gui.GuiNormal
Returns the normalization Object
getNormMethod() - Method in class halo.userinterface.gui.session.Session
Returns the name of the normalization method
getNumberExperiments() - Method in class halo.data.Data
Returns the number of measured experiments (not changeable through filtering!).
getOriginalAtts() - Method in class halo.userinterface.gui.GuiFilterData
Returns the attributes from the datafile
getOriginalGene() - Method in class halo.userinterface.gui.GuiFilterData
Returns the original name of the gene attribute
getOriginalLabelsCalls() - Method in class halo.userinterface.gui.session.Session
Returns the list of attributes from the original file (present calls)
getOriginalLabelsOther() - Method in class halo.userinterface.gui.session.Session
Returns the list of attributes from the original file (no present calls)
getPathR() - Method in class halo.userinterface.gui.session.Session
Returns the path to R
getPathToR() - Static method in class halo.userinterface.gui.session.Config
Returns the path of the R bin folder
getPlotName() - Method in class halo.data.Data
Returns the name of the file into which evaluation results will be printed as a plottable table.
getPlotName() - Method in class halo.userinterface.gui.GuiFilterData
Returns the name of the file containing the plotting information for evaluation
getPosX() - Method in class halo.userinterface.gui.session.Session
Returns x position of the window
getPosY() - Method in class halo.userinterface.gui.session.Session
Returns y position of the window
getPqs() - Method in class halo.data.Data
Returns the probe set quality scores.
getPqsMax() - Method in class halo.normalization.Normalization
Returns the highest value of the probe set quality scores
getPreDescr() - Method in class halo.data.Data
Returns the description = column labels of pre-existing RNA.
getPreRNA() - Method in class halo.data.Data
Returns all the values for pre-existing RNA.
getRatio() - Method in class halo.halflife.HalfLife
Returns the ratio values
getRatioMethod() - Method in class halo.userinterface.gui.GuiNormal
Returns the method for ratio calculation
getRatioMethod() - Method in class halo.userinterface.gui.session.Session
Returns the ratio calculation method
getReplicate() - Method in class halo.data.Data
Returns the number of the replicate used for calculations.
getReplicate() - Method in class halo.halflife.HalfLife
Returns the number of the used replicate
getReplicate() - Method in class halo.normalization.Normalization
Returns the replicate for calculation
getReplicate() - Method in class halo.userinterface.gui.session.Session
Returns the constant replicate
getReplicates() - Method in class halo.userinterface.gui.GuiHalfLife
Returns the number of the used replicate for each half-life object
getReplicates() - Method in class halo.userinterface.gui.session.Session
Returns the replicate number used for calculation
getReplicatesTotal() - Method in class halo.data.Data
Returns the total number of replicates.
getSecond() - Method in class halo.tools.Tuple
Returns the second value for the tuple
getSeries() - Method in class halo.userinterface.gui.graphhandler.XYGraphConstructor
Returns the list of series
getSessionFile() - Static method in class halo.userinterface.gui.session.Config
Returns the path of the session file
getSize() - Method in class halo.data.Data
Returns the number of probesets present after filtering.
getSize() - Method in class halo.userinterface.gui.GuiFilterData
Returns the size of the data after the performed filtering steps
getSpot() - Method in class halo.data.Data
Returns the list of spots.
getSpotid() - Method in class halo.data.Data
Returns the name of the column with probeset ids.
getSpotId(U) - Method in class halo.data.Mapping
Retrieves the list of keys for one given attribute
getSpotid() - Method in class halo.userinterface.gui.GuiFilterData
Returns the name of the column with spotIDs
getTimes() - Method in class halo.userinterface.gui.GuiHalfLife
Returns the list of time points used for calculation
getTimes() - Method in class halo.userinterface.gui.session.Session
Returns the list of time points used for half-life calculation
getTotalDescr() - Method in class halo.data.Data
Returns the description = column labeles of total RNA.
getTotalRNA() - Method in class halo.data.Data
Returns all the values for total RNA.
getUserbrowser() - Static method in class halo.userinterface.gui.session.Config
Returns the user browser
GraphHandler - Class in halo.userinterface.gui.graphhandler
Provides methods for the generation and handling of graphs created with JFreeChart.
GraphHandler() - Constructor for class halo.userinterface.gui.graphhandler.GraphHandler
 
Gui - Class in halo.userinterface.gui
Graphical User Interface for half-life calculation and additional methods
Gui() - Constructor for class halo.userinterface.gui.Gui
Generate GUI object, start initializing
GuiFilterData - Class in halo.userinterface.gui
'Interface' which connects GUI and loading/filtering methods for data
GuiFilterData() - Constructor for class halo.userinterface.gui.GuiFilterData
Constructor creating an object of GuiFilterData
GuiHalfLife - Class in halo.userinterface.gui
'Interface' which connects GUI and methods for half-life calculations
GuiHalfLife() - Constructor for class halo.userinterface.gui.GuiHalfLife
 
GuiNormal - Class in halo.userinterface.gui
'Interface' which connects GUI and methods for normalization
GuiNormal() - Constructor for class halo.userinterface.gui.GuiNormal
 
GuiTools - Class in halo.userinterface.gui.guitools
Class containing several tools used for Graphical User Interface
GuiTools() - Constructor for class halo.userinterface.gui.guitools.GuiTools
 

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