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

H

HalfLife - Class in halo.halflife
Calculation of half-lives and median-based Correction Factors
HalfLife() - Constructor for class halo.halflife.HalfLife
Constructs a HalfLife object with default Alpha
HALFLIFE - Static variable in class halo.halflife.HalfLifeWriter
 
HalfLife_New - Class in halo.halflife
Implementation of HalfLife providing methods for the usual calculation of half-life values for newly transcribed RNA, based on the ratio of newly transcribed to total RNA
HalfLife_New() - Constructor for class halo.halflife.HalfLife_New
 
HalfLife_NewPre - Class in halo.halflife
Class that provides half-life calculation methods based on the ratio of newly transcribed (labeled) RNA to pre-existing (unlabeled)RNA
HalfLife_NewPre() - Constructor for class halo.halflife.HalfLife_NewPre
 
HalfLife_Pre - Class in halo.halflife
Implementation of HalfLife providing methods for the usual calculation of half-life values for pre-existing RNA, based on the ratio of pre-existing to total RNA
HalfLife_Pre() - Constructor for class halo.halflife.HalfLife_Pre
 
HalfLifeWriter - Class in halo.halflife
Class for exporting half-life values
HalfLifeWriter(String, String, int, HalfLife...) - Constructor for class halo.halflife.HalfLifeWriter
Writes the half-life values of a number of different HalfLife objects into a file, thereby giving the choice to eliminate lines that are not saturated
halo.data - package halo.data
Provides for the extraction, filtering, handling and saving of expression data.
halo.data.biascorrection - package halo.data.biascorrection
Provides for the correction of bias in the expression data.
halo.data.dataExceptions - package halo.data.dataExceptions
Provides exceptions for incorrect data file format Related Documentation For overviews, tutorials, examples, guides, and tool documentation, please see: HALO documentation halo.examples - package halo.examples
Provides easy-to-understand examples for the usage of HALO.
halo.halflife - package halo.halflife
Provides for the calculation and handling of half-lives.
halo.halflife.alpha - package halo.halflife.alpha
Provides for the calculation of alpha functions.
halo.normalization - package halo.normalization
Provides for the calculation and handling of normalization.
halo.tools - package halo.tools
Provides a set of tools applicable for several uses.
halo.userinterface.cmdline - package halo.userinterface.cmdline
Provides for the handling of user input and starting of corresponding calculations.
halo.userinterface.cmdline.cmdexceptions - package halo.userinterface.cmdline.cmdexceptions
Provides exceptions for incorrect user input.
halo.userinterface.gui - package 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 - package halo.userinterface.gui.graphhandler
Provides for generation of plots and histograms.
halo.userinterface.gui.guitools - package halo.userinterface.gui.guitools
Provides a set of tools corresponding to the graphical user interface.
halo.userinterface.gui.session - package halo.userinterface.gui.session
Provides for the handling, saving and loading of sessions and configuration information.
hasData() - Method in class halo.userinterface.gui.GuiFilterData
Checks whether Data has been set
hasGeneNames() - Method in class halo.userinterface.gui.GuiFilterData
Checks whether the attribute containing gene names for each spot has been set
hasGenes() - Method in class halo.userinterface.gui.GuiFilterData
Checks whether the multiple fasta file containing the sequences has been set and whether the attribute describing the gene names for each spot exists
hasHL() - Method in class halo.userinterface.gui.GuiHalfLife
Checks whether there are any half-lives
hasLineColumns(String, int) - Static method in class halo.tools.Tools
Checks whether a line consists of at least the given number of columns, whereas columns are separated through any whitespace sign
hasNormalization() - Method in class halo.userinterface.gui.GuiFilterData
Checks whether normalization has been performed
hasNormalization() - Method in class halo.userinterface.gui.GuiNormal
Checks whether normalization has been performed
HelpButton - Class in halo.userinterface.gui.guitools
Provides a button that displays a help dialog upon clicking.
HelpButton(String) - Constructor for class halo.userinterface.gui.guitools.HelpButton
Constructs a new help button
HistogramConstructor - Class in halo.userinterface.gui.graphhandler
Provides methods for the construction and handling of histograms.
HistogramConstructor(String, String, String) - Constructor for class halo.userinterface.gui.graphhandler.HistogramConstructor
Constructs a new histogram constructor object
HOMEPAGE - Static variable in class halo.tools.Tools
 
HOMEPAGEDOC - Static variable in class halo.tools.Tools
 

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