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

F

FastaFileData - Class in util
 
FastaFileData() - Constructor for class util.FastaFileData
 
fatalErrorExit(String) - Method in class startup.ParameterFileParser
Method which displays the given string and then exists the program, due to the fact that one of the parameters could not be parsed.
FeatureException - Exception in util
 
FeatureException() - Constructor for exception util.FeatureException
 
FeatureException(String) - Constructor for exception util.FeatureException
 
FeatureExtractionException - Exception in util.classificationFeatures
This exception represents the errors that can occur when features are extracted.
FeatureExtractionException() - Constructor for exception util.classificationFeatures.FeatureExtractionException
 
FeatureExtractionException(String) - Constructor for exception util.classificationFeatures.FeatureExtractionException
 
FeatureExtractionExtension - Class in util
 
FeatureExtractionExtension() - Constructor for class util.FeatureExtractionExtension
 
FeatureFileContent - Class in var.featureSelection
 
FeatureFileContent() - Constructor for class var.featureSelection.FeatureFileContent
 
FeatureRecognition - Class in startup.features
Class designed to take care of selected features by a feature selection algorithm.
FeatureRecognition(Logger, String, String, String, String, int) - Constructor for class startup.features.FeatureRecognition
constructor.
FeatureRecognition(Logger, String, String, int) - Constructor for class startup.features.FeatureRecognition
Constructor.
FeatureRecognition.TARGET - Enum in startup.features
What action to do: a) WRITE_SVG : simply make an SVG picture of the features.
FeatureSelectionStub - Class in util.featureSelection
 
FeatureSelectionStub(ClassificationAction, Logger) - Constructor for class util.featureSelection.FeatureSelectionStub
 
FeatureSelectionStub.FEATURE_SELECTION_PURPOSE - Enum in util.featureSelection
 
FeatureSelectionStub.FEATURE_SELECTION_TYPE - Enum in util.featureSelection
 
FeatureSelectionSupport - Class in util.featureSelection
This class provides the means to investigate the possible regulatory features indicated by the features that are selected by feature selection methods.
FeatureSelectionSupport(String, String, String, String) - Constructor for class util.featureSelection.FeatureSelectionSupport
 
FibonacciSwitchConversion - Class in util.conversions.implementations
 
FibonacciSwitchConversion() - Constructor for class util.conversions.implementations.FibonacciSwitchConversion
 
FileInfo - Class in util
 
FileInfo() - Constructor for class util.FileInfo
 
FileParser - Class in util.io
Utility class for parsing and extracting data from files
FileParser() - Constructor for class util.io.FileParser
 
FileUtils - Class in util.io
Util class which contains some necessary but rather specific I/O methods (mostly file I/O) for the JASPr code.
FileUtils() - Constructor for class util.io.FileUtils
 
fillClassificationAction() - Method in class startup.gui.SprClassificationActionPanel
 
fillCrossValFiles(int, int, File, File, boolean) - Static method in class util.io.FileUtils
 
fillCrossValTrainingFile(int, int, int, File, File, boolean) - Static method in class util.io.FileUtils
Creates and fills the temporary file with data for crossvalidation.
FILTER_NONE - Static variable in class classifier.wekaSVM.SMO
filter: No normalization/standardization
FILTER_NORMALIZE - Static variable in class classifier.wekaSVM.SMO
filter: Normalize training data
FILTER_STANDARDIZE - Static variable in class classifier.wekaSVM.SMO
filter: Standardize training data
filterEMBLSeq(String) - Method in class util.parsers.ExtractTrainingData
 
filterTypeTipText() - Method in class classifier.wekaSVM.SMO
Returns the tip text for this property
findClassificationSites(List<ClassificationFeature>) - Method in class util.featureSelection.FeatureSelectionSupport
 
findSupport - Variable in class util.classificationFeatures.AttributeDescription
 
FixedOption - Class in var.experimenter
 
FixedOption() - Constructor for class var.experimenter.FixedOption
 
FixedOption(String) - Constructor for class var.experimenter.FixedOption
 
FixedRangeOption - Class in var.experimenter
 
FixedRangeOption() - Constructor for class var.experimenter.FixedRangeOption
 
FSCompare - Class in var
This class is meant to find comparable results between featureselection filters of the full type.
FSCompare(String[]) - Constructor for class var.FSCompare
 
FSDraw - Class in var
 
FSDraw() - Constructor for class var.FSDraw
 
FunSiP - Class in main
This class is a Java implementation of the splicemachine code, used for splice site prediction in the annotation pipeline.
FunSiP(String[]) - Constructor for class main.FunSiP
The main launcher object for the project.
FunSiPFeatures - Class in main
The goal of this program - part of the FunSiP-package - is to evaluate, study and display the various features that were selected and scored by the possible feature selection algorithms.
FunSiPFeatures(String[]) - Constructor for class main.FunSiPFeatures
Constructor of the FunSiPFeatures program.
FunSiPGui - Class in main
This class consists of the building blocks for a graphical representation of the FunSiP program.
FunSiPGui() - Constructor for class main.FunSiPGui
Constructor for the graphical framework.
FunSiPJar - Class in main
This class is just meant as the main-contact point when the jar-file is launched.
FunSiPJar(String[]) - Constructor for class main.FunSiPJar
Constructor method for FunSiPJar.
FunSiPResultGui - Class in main
This class is used for testing purposes of FunSiP only.
FunSiPResultGui(String, String) - Constructor for class main.FunSiPResultGui
The constructor for the program.
FunSiPWorkflow - Class in startup
This class represents the different actions etc. defined in a single configuration file.
FunSiPWorkflow(Logger, String) - Constructor for class startup.FunSiPWorkflow
Constructor, does nothing really but assigning the provided method parameters to local variables.
FunSiPWorkflow.MULTITHREADING - Enum in startup
The different types of available multithreading: a) NO_MULTITHREADING : no multithreading at all b) SINGLE_PC_MULTITHREADING : launches each different ClassificationAction in a seperate thread, and waits until they're all finished; c) CLUSTER_MULTITHREADING : attempts to launch each ClassificationAction in a seperate job for the cluster (standard qsub-command).

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