Uses of Class
de.jstacs.results.Result

Packages that use Result

Package	Description
de.jstacs.algorithms.alignment	Provides classes for alignments.
de.jstacs.classifiers	This package provides the framework for any classifier.
de.jstacs.classifiers.assessment	This package allows to assess classifiers. It contains the class ClassifierAssessment that is used as a super-class of all implemented methodologies of an assessment to assess classifiers.
de.jstacs.data.sequences.annotation	Provides the facilities to annotate Sequences using a number of pre-defined annotation types, or additional implementations of the SequenceAnnotation class.
de.jstacs.results	This package provides classes for results and sets of results.
de.jstacs.results.savers
de.jstacs.tools
de.jstacs.tools.ui.galaxy

Uses of Result in de.jstacs.algorithms.alignment

Methods in de.jstacs.algorithms.alignment that return Result

Modifier and Type	Method and Description
Result	StringAlignment.getAnnotationResult() Returns the annotation result.

Constructors in de.jstacs.algorithms.alignment with parameters of type Result

Constructor and Description
StringAlignment(double cost, String[] strings, Result res) This constructor creates an instance storing the aligned Strings and the costs of the alignment.

Uses of Result in de.jstacs.classifiers

Subclasses of Result in de.jstacs.classifiers

Modifier and Type	Class and Description
static class	AbstractScoreBasedClassifier.DoubleTableResult This class is for Results given as a table of double s.

Uses of Result in de.jstacs.classifiers.assessment

Methods in de.jstacs.classifiers.assessment that return types with arguments of type Result

Modifier and Type	Method and Description
Collection<Result>	Sampled_RepeatedHoldOutAssessParameterSet.getAnnotation()
Collection<Result>	RepeatedSubSamplingAssessParameterSet.getAnnotation()
Collection<Result>	RepeatedHoldOutAssessParameterSet.getAnnotation()
ArrayList<Result>	KFoldCrossValidationAssessParameterSet.getAnnotation()
Collection<Result>	ClassifierAssessmentAssessParameterSet.getAnnotation() Returns a Collection of parameters containing informations about this ClassifierAssessmentAssessParameterSet.

Uses of Result in de.jstacs.data.sequences.annotation

Methods in de.jstacs.data.sequences.annotation that return Result

Modifier and Type	Method and Description
Result[]	SequenceAnnotation.getAnnotations() Returns the additional annotations of this SequenceAnnotation as given in the constructor.

Constructors in de.jstacs.data.sequences.annotation with parameters of type Result

Constructor and Description
CisRegulatoryModuleAnnotation(String identifier, MotifAnnotation[] motifs, Result... additionalAnnotation) Creates a new CisRegulatoryModuleAnnotation from a set of motifs and possibly additional annotations.
IntronAnnotation(String identifier, SinglePositionSequenceAnnotation donor, SinglePositionSequenceAnnotation acceptor, Result... additionalAnnotation) Creates a new IntronAnnotation from a donor SinglePositionSequenceAnnotation and an acceptor SinglePositionSequenceAnnotation and a set of additional annotations.
LocatedSequenceAnnotation(int position, String type, String identifier, Result... results) Creates a new LocatedSequenceAnnotation of type type with identifier identifier and additional annotation (that does not fit the SequenceAnnotation definitions) given as an array of Results result.
LocatedSequenceAnnotation(int position, String type, String identifier, SequenceAnnotation[] annotations, Result... additionalAnnotation) Creates a new LocatedSequenceAnnotation of type type with identifier identifier, additional annotation (that does not fit the SequenceAnnotation definitions) given as an array of Results additionalAnnotation and sub-annotations annotations.
LocatedSequenceAnnotation(String type, String identifier, LocatedSequenceAnnotation[] annotations, Result... additionalAnnotation) Creates a new LocatedSequenceAnnotation of type type with identifier identifier, additional annotation (that does not fit the SequenceAnnotation definitions) given as an array of Results additionalAnnotation and sub-annotations annotations.
LocatedSequenceAnnotationWithLength(int position, int length, String type, String identifier, Result... results) Creates a new LocatedSequenceAnnotationWithLength of type type with identifier identifier and additional annotation (that does not fit the SequenceAnnotation definitions) given as an array of Results result.
LocatedSequenceAnnotationWithLength(int position, int length, String type, String identifier, SequenceAnnotation[] annotations, Result... additionalAnnotations) Creates a new LocatedSequenceAnnotationWithLength of type type with identifier identifier, additional annotation (that does not fit the SequenceAnnotation definitions) given as an array of Results additionalAnnotations and sub-annotations annotations.
LocatedSequenceAnnotationWithLength(String type, String identifier, LocatedSequenceAnnotation[] annotations, Result... additionalAnnotations) Creates a new LocatedSequenceAnnotationWithLength of type type with identifier identifier, additional annotation (that does not fit the SequenceAnnotation definitions) given as an array of Results additionalAnnotations and sub-annotations annotations.
MotifAnnotation(String identifier, int position, int length, StrandedLocatedSequenceAnnotationWithLength.Strand strandedness, Result... additionalAnnotation) Creates a new MotifAnnotation of type type with identifier identifier and additional annotation (that does not fit the SequenceAnnotation definitions) given as an array of Results additionalAnnotation.
ReferenceSequenceAnnotation(String identifier, Sequence ref, Result... results) Creates a new ReferenceSequenceAnnotation with identifier identifier, reference sequence ref, and additional annotation (that does not fit the SequenceAnnotation definitions) given as a Result result.
SequenceAnnotation(String type, String identifier, Result result) Creates a new SequenceAnnotation of type type with identifier identifier and additional annotation (that does not fit the SequenceAnnotation definitions) given as a Result result.
SequenceAnnotation(String type, String identifier, Result[]... results) Creates a new SequenceAnnotation of type type with identifier identifier and additional annotation (that does not fit the SequenceAnnotation definitions) given as an array of Results results.
SequenceAnnotation(String type, String identifier, SequenceAnnotation[] subAnnotations, Result... additionalAnnotation) Creates a new SequenceAnnotation of type type with identifier identifier and additional annotation (that does not fit the SequenceAnnotation definitions) given as an array of Results additionalAnnotation.
SinglePositionSequenceAnnotation(SinglePositionSequenceAnnotation.Type type, String identifier, int position, Result... additionalAnnotation) Creates a new SinglePositionSequenceAnnotation of type type with identifier identifier, position position and additional annotations additionalAnnotation.
StrandedLocatedSequenceAnnotationWithLength(int position, int length, StrandedLocatedSequenceAnnotationWithLength.Strand strandedness, String type, String identifier, Result... results) Creates a new StrandedLocatedSequenceAnnotationWithLength of type type with identifier identifier and additional annotation (that does not fit the SequenceAnnotation definitions) given as an array of Results results.
StrandedLocatedSequenceAnnotationWithLength(int position, int length, StrandedLocatedSequenceAnnotationWithLength.Strand strandedness, String type, String identifier, SequenceAnnotation[] annotations, Result... additionalAnnotations) Creates a new StrandedLocatedSequenceAnnotationWithLength of type type with identifier identifier, additional annotation (that does not fit the SequenceAnnotation definitions) given as an array of Results additionalAnnotations and sub-annotations annotations.
StrandedLocatedSequenceAnnotationWithLength(String type, String identifier, StrandedLocatedSequenceAnnotationWithLength.Strand strandedness, LocatedSequenceAnnotation[] annotations, Result... additionalAnnotations) Creates a new StrandedLocatedSequenceAnnotationWithLength of type type with identifier identifier, additional annotation (that does not fit the SequenceAnnotation definitions) given as an array of Results additionalAnnotations and sub-annotations annotations.

Constructor parameters in de.jstacs.data.sequences.annotation with type arguments of type Result

Constructor and Description
LocatedSequenceAnnotation(int position, String type, String identifier, Collection<Result> results) Creates a new LocatedSequenceAnnotation of type type with identifier identifier and additional annotation (that does not fit the SequenceAnnotation definitions) given as a Collection of Results result.
LocatedSequenceAnnotationWithLength(int position, int length, String type, String identifier, Collection<Result> results) Creates a new LocatedSequenceAnnotationWithLength of type type with identifier identifier and additional annotation (that does not fit the SequenceAnnotation definitions) given as a Collection of Results result.
SequenceAnnotation(String type, String identifier, Collection<? extends Result> results) Creates a new SequenceAnnotation of type type with identifier identifier and additional annotation (that does not fit the SequenceAnnotation definitions) given as a Collection of Results results.
StrandedLocatedSequenceAnnotationWithLength(int position, int length, StrandedLocatedSequenceAnnotationWithLength.Strand strandedness, String type, String identifier, Collection<Result> results) Creates a new StrandedLocatedSequenceAnnotationWithLength of type type with identifier identifier and additional annotation (that does not fit the SequenceAnnotation definitions) given as a Collection of Results results.

Uses of Result in de.jstacs.results

Subclasses of Result in de.jstacs.results

Modifier and Type	Class and Description
class	CategoricalResult A class for categorical results (i.e.
class	DataSetResult Result that contains a DataSet.
class	ImageResult A class for results that are images of the PNG format.
class	ListResult Class for a Result that contains a list or a matrix, respectively, of ResultSets.
class	NumericalResult Class for numerical Result values.
class	PlotGeneratorResult Class for a Result that may be used to generate plots for different output formats using GraphicsAdaptor sub-classes.
class	ResultSetResult Class for a Result that contains a single ResultSet.
class	SimpleResult Abstract class for a Result with a value of a primitive data type or String.
class	StorableResult Class for Results that are Storables.
class	TextResult Class for a result that is basically a text file (or its contents).

Fields in de.jstacs.results with type parameters of type Result

Modifier and Type	Field and Description
protected AnnotatedEntityList<Result>	ResultSet.results The internally stores results.

Methods in de.jstacs.results that return Result

Modifier and Type	Method and Description
static Result	Result.createResult(String name, String comment, DataType datatype, Object value) Factory method to create a new Result.
Result	ResultSet.getResultAt(int index) Returns Result number index in this ResultSet.
Result	ResultSet.getResultForName(String name) Returns Result with name name in this ResultSet.
Result[]	ResultSet.getResults() Returns all internal results as an array of Results.

Methods in de.jstacs.results with parameters of type Result

Modifier and Type	Method and Description
boolean	Result.isCastableResult(Result test) Returns true if the data type of the Result test can be casted to that of this instance and both have the same name and comment for the Result.
boolean	Result.isComparableResult(Result test) Returns true if the Result test and the current object have the same data type, name and comment for the result.

Constructors in de.jstacs.results with parameters of type Result

Constructor and Description
ResultSet(Result result) Constructs a new ResultSet containing one Result.
ResultSet(Result[]... results) Constructs a new ResultSet from a two-dimensional array of Results.

Constructor parameters in de.jstacs.results with type arguments of type Result

Constructor and Description
ResultSet(Collection<? extends Result> results) Constructs a new ResultSet from a Collection of type Result.

Uses of Result in de.jstacs.results.savers

Classes in de.jstacs.results.savers with type parameters of type Result

Modifier and Type	Interface and Description
interface	ResultSaver<T extends Result> Interface for saving Results to a file.

Methods in de.jstacs.results.savers with type parameters of type Result

Modifier and Type	Method and Description
static <T extends Result> ResultSaver<T>	ResultSaverLibrary.getSaver(Class<? extends T> resultClass) Returns the most suitable ResultSaver (if any) currently registered in the library.
static <T extends Result> void	ResultSaverLibrary.register(Class<? extends T> clazz, ResultSaver<T> saver) Registers the supplied ResultSaver for the given class in the library.

Uses of Result in de.jstacs.tools

Subclasses of Result in de.jstacs.tools

Modifier and Type	Class and Description
class	ToolResult Class for the results of a JstacsTool.

Methods in de.jstacs.tools that return types with arguments of type Result

Modifier and Type	Method and Description
Class<? extends Result>	JstacsTool.ResultEntry.getDeclaredClass() Returns the class declared for the default result.

Constructor parameters in de.jstacs.tools with type arguments of type Result

Constructor and Description
JstacsTool.ResultEntry(Class<? extends Result> clazz, String format, String name) Creates a new default result entry.

Uses of Result in de.jstacs.tools.ui.galaxy

Subclasses of Result in de.jstacs.tools.ui.galaxy

Modifier and Type	Class and Description
static class	GalaxyAdaptor.FileResult Result for files that are results of some computation.
static class	GalaxyAdaptor.HeadResult Class for a result that is basically a CategoricalResult, but has its own name for checking purposes.
static class	GalaxyAdaptor.LineBasedResult Superclass for all Result that may be saved line by line.
static class	GalaxyAdaptor.LinkedImageResult Class for an ImageResult that is linked to a file that can be downloaded.

Methods in de.jstacs.tools.ui.galaxy with parameters of type Result

Modifier and Type	Method and Description
void	GalaxyAdaptor.addResult(Result res, boolean export, boolean includeInSummary) Adds a result to the results of a program run.
void	GalaxyAdaptor.addResult(Result res, boolean export, boolean includeInSummary, String exportExtension) Adds a result to the results of a program run.
String	GalaxyAdaptor.export(String filename, Result res, String exportExtension) Exports a specified Result of a program execution to a file provided by filename and returns the corresponding Galaxy data type.

Method parameters in de.jstacs.tools.ui.galaxy with type arguments of type Result

Modifier and Type	Method and Description
static String	GalaxyAdaptor.getDefaultExtension(Class<? extends Result> resClass) Returns the default extension (Galaxy format) for a given result class.