Version history: Difference between revisions

From Jstacs
Jump to navigationJump to search
No edit summary
 
(29 intermediate revisions by 2 users not shown)
Line 1: Line 1:
''September 8, 2008'':<br />
This page briefly summarizes the changes in Jstacs. Each release is listed as separate section.
 
== Jstacs 2.3 (''released September 8, 2017'')==
 
=== New classes and packages ===
* Jstacs 2.3 is the first release to be accompanied by [http://www.jstacs.de/api-fx/index.html JstacsFX], a library for building JavaFX-based graphical user interfaces based on [http://www.jstacs.de/api-2.3/de/jstacs/tools/JstacsTool.html JstacsTools]
* new interface [http://www.jstacs.de/api-2.3/de/jstacs/algorithms/optimization/MultiThreadedFunction.html MultiThreadedFunction]
* new class [http://www.jstacs.de/api-2.3/de/jstacs/utils/LargeSequenceReader.html LargeSequenceReader] for reading large sequence files in chunks
* new interface [http://www.jstacs.de/api-2.3/de/jstacs/sequenceScores/QuickScanningSequenceScore.html QuickScanningSequenceScore]
* new class [http://www.jstacs.de/api-2.3/de/jstacs/parameters/validation/RegExpValidator.html RegExpValidator] for checking String inputs against a regular expression
* new class [http://www.jstacs.de/api-2.3/de/jstacs/data/alphabets/IUPACDNAAlphabet.html IUPACDNAAlphabet]
 
=== New features and improvements ===
* [http://www.jstacs.de/api-2.3/de/jstacs/algorithms/alignment/Alignment.html Alignments] may now handle different [http://www.jstacs.de/api-2.3/de/jstacs/algorithms/alignment/cost/Costs.html costs] for insert and delete gaps
* [http://www.jstacs.de/api-2.3/de/jstacs/results/ListResult.html ListResults] may now be constructed from Collections of [http://www.jstacs.de/api-2.3/index.html ResultSets]
* Several minor improvements and bugfixes in many classes
* Improvements of documentation of several classes
 
== Jstacs 2.2 (''released February 12, 2016'')==
 
=== New classes and packages ===
* [http://www.jstacs.de/api-2.2/de/jstacs/classifiers/performanceMeasures/CorrelationCoefficient.html CorreationCoefficient] PerformanceMeasure
* [http://www.jstacs.de/api-2.2/de/jstacs/clustering/hierachical/package-summary.html de.jstacs.clustering] package with classes for hierarchical clustering
* [http://www.jstacs.de/api-2.2/de/jstacs/data/DeBruijnGraphSequenceGenerator.html DeBruijnGraphSequenceGenerator] and [http://www.jstacs.de/api-2.2/de/jstacs/data/DeBruijnSequenceGenerator.html DeBruijnSequenceGenerator] for generating De Buijn sequences
* [http://www.jstacs.de/api-2.2/de/jstacs/data/sequences/CyclicSequenceAdaptor.html CyclicSequenceAdaptor] for representing cyclic sequences
* [http://www.jstacs.de/api-2.2/de/jstacs/results/PlotGeneratorResult.html PlotGeneratorResult] for representing results that plot images to a Graphics2D object
* [http://www.jstacs.de/api-2.2/de/jstacs/results/TextResult.html TextResult] for results that may be stored as text files
* package [http://www.jstacs.de/api-2.2/de/jstacs/results/savers/package-summary.html de.jstacs.results.savers] for generic classes that store results to disk
* [http://www.jstacs.de/api-2.2/de/jstacs/sequenceScores/statisticalModels/differentiable/localMixture/LimitedSparseLocalInhomogeneousMixtureDiffSM_higherOrder.html LimitedSparseLocalInhomogeneousMixtureDiffSM_higherOrder] for sparse local inhomogeneous mixture (Slim) models
* [http://www.jstacs.de/api-2.2/de/jstacs/sequenceScores/statisticalModels/trainable/PFMWrapperTrainSM.html PFMWrapperTrainSM] for representing position frequency matrices and position weight matrices from databases
* package [http://www.jstacs.de/api-2.2/de/jstacs/tools/package-summary.html de.jstacs.tools] with classes for generic Jstacs tools that may be used in different user interfaces ([http://www.jstacs.de/api-2.2/de/jstacs/tools/ui/cli/CLI.html command line], [http://www.jstacs.de/api-2.2/de/jstacs/tools/ui/galaxy/Galaxy.html Galaxy], JavaFX)
* [http://www.jstacs.de/api-2.2/de/jstacs/utils/Compression.html Compression] for ZIP compression of Strings
* package [http://www.jstacs.de/api-2.2/de/jstacs/utils/graphics/package-summary.html de.jstacs.utils.graphics] with generic [http://www.jstacs.de/api-2.2/de/jstacs/utils/graphics/GraphicsAdaptor.html GraphicsAdaptor] using Apache XML commons
* projects: Dimont, GeMoMa, Slim, TALEN, motif comparison
 
=== New features and improvements ===
 
* Major restructuring of [http://www.jstacs.de/api-2.2/de/jstacs/algorithms/alignment/Alignment.html Alignment] for better efficiency
* Alignment [http://www.jstacs.de/api-2.2/de/jstacs/algorithms/alignment/cost/Costs.html Costs] and [http://www.jstacs.de/api-2.2/de/jstacs/algorithms/alignment/StringAlignment.html StringAlignment] now [http://www.jstacs.de/api-2.2/de/jstacs/Storable.html Storable]
* New constructor of [http://www.jstacs.de/api-2.2/de/jstacs/data/DataSet.html#DataSet(de.jstacs.data.AlphabetContainer,%20de.jstacs.io.AbstractStringExtractor,%20java.lang.String,%20int,%20double) DataSet] allowing a specified percentage of sequences to mismatch the given alphabet
* [http://www.jstacs.de/api-2.2/de/jstacs/data/bioJava/BioJavaAdapter.html BioJavaAdapter] ported to BioJava 1.9
* [http://www.jstacs.de/api-2.2/de/jstacs/io/XMLParser.html XMLParser] now also allows for storing [http://www.jstacs.de/api-2.2/de/jstacs/data/sequences/Sequence.html Sequences]
* New method for parsing HMMer profile HMMs in [http://www.jstacs.de/api-2.2/de/jstacs/sequenceScores/statisticalModels/trainable/hmm/HMMFactory.html#parseProfileHMMFromHMMer(java.io.Reader,%20java.lang.StringBuffer,%20java.util.LinkedList,%20java.util.LinkedList) HMMFactory]
* Several minor improvements and bugfixes in many classes
* Improvements of documentation of several classes
 
== Jstacs 2.1 (''released Mai 31, 2013'')==
 
=== New classes ===
* [http://www.jstacs.de/api-2.1/de/jstacs/algorithms/optimization/termination/MultipleIterationsCondition.html MultipleIterationsCondition]: Requires another TerminationCondition to fail a contiguous, specified number of times
* [http://www.jstacs.de/api-2.1/de/jstacs/classifiers/ClassifierFactory.html ClassifierFactory]: Allows for creating standard classifiers
* [http://www.jstacs.de/api-2.1/de/jstacs/utils/SeqLogoPlotter.html SeqLogoPlotter]: Plot PNG sequence logos from within Jstacs
* [http://www.jstacs.de/api-2.1/de/jstacs/sequenceScores/statisticalModels/trainable/hmm/states/emissions/continuous/MultivariateGaussianEmission.html MultivariateGaussianEmission]: Multivariate Gaussian emission density for a Hidden Markov Model
* [http://www.jstacs.de/api-2.1/de/jstacs/sequenceScores/statisticalModels/trainable/discrete/inhomogeneous/MEManager.html MEManager]: Maximum entropy model
 
=== New features and improvements ===
* [http://www.jstacs.de/api-2.1/de/jstacs/algorithms/alignment/Alignment.html Alignment]: Added [http://www.jstacs.de/api-2.1/de/jstacs/algorithms/alignment/Alignment.AlignmentType.html#FREE_SHIFT free shift] alignment
* [http://www.jstacs.de/api-2.1/de/jstacs/classifiers/performanceMeasures/PerformanceMeasure.html PerformanceMeasure] and sub-classes: Extension to weighted test data
* [http://www.jstacs.de/api-2.1/de/jstacs/data/alphabets/DNAAlphabet.html DNAAlphabet]: Parser speed-up
* [http://www.jstacs.de/api-2.1/de/jstacs/utils/PFMComparator.html PFMComparator]: Extension to PFM from other sources/databases
* [http://www.jstacs.de/api-2.1/de/jstacs/utils/ToolBox.html ToolBox]: New convenience methods for computing several statistics (e.g., median, correlation)
* [http://www.jstacs.de/api-2.1/de/jstacs/motifDiscovery/SignificantMotifOccurrencesFinder.html SignificantMotifOccurrencesFinder]: New methods for computing PWMs and statistics from predictions
* [http://www.jstacs.de/api-2.1/de/jstacs/sequenceScores/SequenceScore.html SequenceScore] and sub-classes: New method toString(NumberFormat)
* [http://www.jstacs.de/api-2.1/de/jstacs/classifiers/AbstractClassifier.html AbstractClassifier], [http://www.jstacs.de/api-2.1/de/jstacs/classifiers/assessment/ClassifierAssessment.html ClassifierAssessment] and sub-classes: Adaption to weighted [http://www.jstacs.de/api-2.1/de/jstacs/classifiers/performanceMeasures/PerformanceMeasure.html PerformanceMeasures]
* [http://www.jstacs.de/api-2.1/de/jstacs/data/DataSet.html DataSet]: Adaption to weighted data, e.g., partitioning
* [http://www.jstacs.de/api-2.1/de/jstacs/utils/REnvironment.html REnvironment]: Changed several methods from String to CharSequence
 
=== Restructuring: ===
* changed MultiDimensionalSequenceWrapperDiffSM to [http://www.jstacs.de/api-2.1/de/jstacs/sequenceScores/differentiable/MultiDimensionalSequenceWrapperDiffSS.html MultiDimensionalSequenceWrapperDiffSS]
 
Several minor new features, bug fixes, and code cleanups
 
== Jstacs 2.0 (''released February 2, 2012'')==
 
''Jstacs 2.0 changes many names and the structure of several packages. It is not code-compatible with Jstacs 1.5 and earlier''
 
=== Restructuring and Renaming ===
* former ScoringFunction, NormalizableScoringFunction, Model
** new base-interface [http://www.jstacs.de/api-2.0/de/jstacs/sequenceScores/SequenceScore.html SequenceScore]
** new sub-interface [http://www.jstacs.de/api-2.0/de/jstacs/sequenceScores/statisticalModels/StatisticalModel.html StatisticalModel] of [http://www.jstacs.de/api-2.0/de/jstacs/sequenceScores/SequenceScore.html SequenceScore] for all statistical models with sub-iterfaces [http://www.jstacs.de/api-2.0/de/jstacs/sequenceScores/statisticalModels/differentiable/DifferentiableStatisticalModel.html DifferentiableStatisticalModel] and [http://www.jstacs.de/api-2.0/de/jstacs/sequenceScores/statisticalModels/trainable/TrainableStatisticalModel.html TrainableStatisticalModel]
** new interface [http://www.jstacs.de/api-2.0/de/jstacs/sequenceScores/differentiable/DifferentiableSequenceScore.html DifferentiableSequenceScore] replaces ScoringFunction
** new interface [http://www.jstacs.de/api-2.0/de/jstacs/sequenceScores/statisticalModels/differentiable/DifferentiableStatisticalModel.html DifferentiableStatisticalModel] replaces NormalizableScoringFunction
** new interface [http://www.jstacs.de/api-2.0/de/jstacs/sequenceScores/statisticalModels/trainable/TrainableStatisticalModel.html TrainableStatisticalModel] replaces Model
** new abstract class [http://www.jstacs.de/api-2.0/de/jstacs/sequenceScores/differentiable/AbstractDifferentiableSequenceScore.html AbstractDifferentiableSequenceScore]
** new abstract class [http://www.jstacs.de/api-2.0/de/jstacs/sequenceScores/statisticalModels/differentiable/AbstractDifferentiableStatisticalModel.html AbstractDifferentiableStatisticalModel] replaces AbstractNormalizableScoringFunction
** new abstract class [http://www.jstacs.de/api-2.0/de/jstacs/sequenceScores/statisticalModels/trainable/AbstractTrainableStatisticalModel.html AbstractTrainableStatisticalModel] replaces AbstractModel
** former *Models renamed to *TrainSM
** former *ScoringFunction renamed to *DiffSS or *DiffSM
** getProbFor removed from TrainableStatisticalModel (former Model) and conceptually replaced by getLogProbFor
** getLogScore(Sequence,int,int) with changed meaning of arguments: getLogScore(Sequence,start,end) instead of getLogScore(Sequence,start,length)
** isTrained() replaced by common method isInitialized()
* Sample renamed to [http://www.jstacs.de/api-2.0/de/jstacs/data/DataSet.html DataSet]
* Parameters and Results
** new super-class of Parameters and Results: [http://www.jstacs.de/api-2.0/de/jstacs/AnnotatedEntity.html AnnotatedEntity]
** common list-type for Parameters and Results: [http://www.jstacs.de/api-2.0/de/jstacs/AnnotatedEntityList.html AnnotatedEntityList]
** Renaming: CollectionParameter -> [http://www.jstacs.de/api-2.0/de/jstacs/parameters/SelectionParameter.html SelectionParameter], MultiSelectionCollectionParameter -> [http://www.jstacs.de/api-2.0/de/jstacs/parameters/MultiSelectionParameter.html MultiSelectionParameter], new super-class [http://www.jstacs.de/api-2.0/de/jstacs/parameters/AbstractSelectionParameter.html AbstractSelectionParameter]
** major refactoring due to common hierarchy and code-cleanup
** lazy evaluation of Parameter/ParameterSet hierarchies moved from ParameterSet (loadParameters()) to [http://www.jstacs.de/api-2.0/de/jstacs/parameters/ParameterSetContainer.html ParameterSetContainer] (constructor on class)
** [http://www.jstacs.de/api-2.0/de/jstacs/utils/SubclassFinder.html SubclassFinder] adapted to lazy evaluation
* performance measures
** new abstract super-class [http://www.jstacs.de/api-2.0/de/jstacs/classifiers/performanceMeasures/AbstractPerformanceMeasure.html AbstractPerformanceMeasure] of all performance measures
** new interface [http://www.jstacs.de/api-2.0/de/jstacs/classifiers/performanceMeasures/NumericalPerformanceMeasure.html NumericalPerformanceMeasure] for all performance measures that return a single number (as opposed, e.g., to curves)
** new class [http://www.jstacs.de/api-2.0/de/jstacs/classifiers/performanceMeasures/PerformanceMeasureParameterSet.html PerformanceMeasureParameterSet] for a collection of general performance measures
** new class [http://www.jstacs.de/api-2.0/de/jstacs/classifiers/performanceMeasures/NumericalPerformanceMeasureParameterSet.html NumericalPerformanceMeasureParameterSet] for a collection of [http://www.jstacs.de/api-2.0/de/jstacs/classifiers/performanceMeasures/NumericalPerformanceMeasure.html NumericalPerformanceMeasure]s
** used in evaluate-method of [http://www.jstacs.de/api-2.0/de/jstacs/classifiers/AbstractClassifier.html AbstractClassifier] and in [http://www.jstacs.de/api-2.0/de/jstacs/classifiers/assessment/ClassifierAssessment.html ClassifierAssessments]
* evaluate and evaluateAll in [http://www.jstacs.de/api-2.0/de/jstacs/classifiers/AbstractClassifier.html AbstractClassifier] joined
* new class [http://www.jstacs.de/api-2.0/de/jstacs/sequenceScores/differentiable/IndependentProductDiffSS.html IndependentProductDiffSS] as super-class of [http://www.jstacs.de/api-2.0/de/jstacs/sequenceScores/statisticalModels/differentiable/IndependentProductDiffSM.html IndepedentProductDiffSM] (former IndependentProductScoringFunction)
* new class [http://www.jstacs.de/api-2.0/de/jstacs/sequenceScores/differentiable/UniformDiffSS.html UniformDiffSS] as super-class of [http://www.jstacs.de/api-2.0/de/jstacs/sequenceScores/statisticalModels/differentiable/UniformDiffSM.html UniformDiffSM] (former UniformScoringFunction)
 
=== New functionality ===
* multi-threaded implementation of Baum-Welch and Viterbi training of hidden Markov models
* new Interface [http://www.jstacs.de/api-2.0/de/jstacs/Singleton.html Singleton] that can be used for singleton instances to save memory, current examples: [http://www.jstacs.de/api-2.0/de/jstacs/data/alphabets/DNAAlphabet.html DNAAlphabet], [http://www.jstacs.de/api-2.0/de/jstacs/data/alphabets/DNAAlphabetContainer.html DNAAlphabetContainer], [http://www.jstacs.de/api-2.0/de/jstacs/data/alphabets/ProteinAlphabet.html ProteinAlphabet]
* added possibility to use NaN-values with [http://www.jstacs.de/api-2.0/de/jstacs/data/alphabets/ContinuousAlphabet.html ContinuousAlphabets]
* added [http://www.jstacs.de/api-2.0/de/jstacs/data/alphabets/ProteinAlphabet.html ProteinAlphabet]
* added [http://www.jstacs.de/api-2.0/de/jstacs/data/sequences/ArbitraryFloatSequence.html ArbitraryFloatSequence] including static methods for [http://www.jstacs.de/api-2.0/de/jstacs/data/DataSet.html DataSet] creation for cases where double-precision is not needed
* new performance measure [http://www.jstacs.de/api-2.0/de/jstacs/classifiers/performanceMeasures/MaximumFMeasure.html MaximumFMeasure]
* access to Parameters in ParameterSets and Results in ResultSets by name
* emitDataSet in [http://www.jstacs.de/api-2.0/de/jstacs/sequenceScores/statisticalModels/differentiable/directedGraphicalModels/BayesianNetworkDiffSM.html BayesianNetworkDiffSM]
* new static method [http://www.jstacs.de/api-2.0/de/jstacs/utils/Time.html#getTimeInstance(java.io.OutputStream) Time.getTimeInstance] that returns UserTime or RealTime depending on availability of shared lib
* [http://www.jstacs.de/api-2.0/de/jstacs/utils/SubclassFinder.html SubclassFinder] allows for adding own base packages
* new method overlaps() in [http://www.jstacs.de/api-2.0/de/jstacs/data/sequences/annotation/LocatedSequenceAnnotationWithLength.html LocatedSequenceAnnotationWithLength]
* [http://www.jstacs.de/api-2.0/de/jstacs/algorithms/optimization/termination/AbstractTerminationCondition.html AbstractTerminationCondition] used in [http://www.jstacs.de/api-2.0/de/jstacs/classifiers/differentiableSequenceScoreBased/ScoreClassifier.html ScoreClassifier] and sub-classes
* public method propagateESS in [http://www.jstacs.de/api-2.0/de/jstacs/sequenceScores/statisticalModels/trainable/hmm/HMMFactory.html HMMFactory]
* new method generateLog in [http://www.jstacs.de/api-2.0/de/jstacs/utils/random/DirichletMRG.html DirichletMRG] for drawing log-values
* added [http://www.jstacs.de/api-2.0/de/jstacs/sequenceScores/statisticalModels/differentiable/DifferentiableStatisticalModelFactory.html DifferentiableStatisticalModelFactory]
 
=== Bugfixes/Improvements ===
* bugfix in propagation of equivalent sample size in [http://www.jstacs.de/api-2.0/de/jstacs/sequenceScores/statisticalModels/trainable/hmm/HMMFactory.html HMMFactory]
* bugfix in random initialization of [http://www.jstacs.de/api-2.0/de/jstacs/sequenceScores/statisticalModels/trainable/hmm/transitions/BasicHigherOrderTransition.html BasicHigherOrderTransition]
* improved [http://www.jstacs.de/api-2.0/de/jstacs/algorithms/alignment/Alignment.html Alignment] implementation
* [http://www.jstacs.de/api-2.0/de/jstacs/utils/SafeOutputStream.html SafeOutputStream] with new static factory method getSafeOutputStream, write methods now work on Objects
 
=== Documentation ===
* improved Javadocs in many classes and packages
* new [[Cookbook]] with extensive documentation and explanation
 
=== Misc ===
* output of [http://www.jstacs.de/api-2.0/de/jstacs/io/NonParsableException.html NonParsableException] more verbose
* Exceptions in multi-threaded code now lead to exit of program instead of only stopping the thread
* update of RServe/RClient
 
== Jstacs 1.5 (''released June 1, 2011'') ==
 
* new package [http://www.jstacs.de/api-1.5/de/jstacs/algorithms/alignment/package-summary.html de.jstacs.algorithms.alignment] for sequence alignment algorithms
* new class [http://www.jstacs.de/api-1.5/de/jstacs/models/ModelFactory.html de.jstacs.models.ModelFactory] with static classes to construct many standard models
* [http://www.jstacs.de/api-1.5/de/jstacs/utils/galaxy/GalaxyAdaptor.html de.jstacs.utils.galaxy.GalaxyAdaptor], an adaptor to [http://galaxy.psu.edu/ Galaxy], which allows for creating Galaxy applications using Jstacs [http://www.jstacs.de/api-1.5/de/jstacs/parameters/ParameterSet.html ParameterSets], also requires new interface [http://www.jstacs.de/api-1.5/de/jstacs/parameters/GalaxyConvertible.html GalaxyConvertible]
* new package [http://www.jstacs.de/api-1.5/de/jstacs/models/hmm/package-summary.html de.jstacs.models.hmm] for a variety of hidden Markov models, which can be learned by different learning principles including generative and discriminative learning principles, maximization and sampling methods
* new package [http://www.jstacs.de/api-1.5/de/jstacs/sampling/package-summary.html de.jstacs.sampling] that contains general infrastructure for parameter sampling
* new class [http://www.jstacs.de/api-1.5/de/jstacs/scoringFunctions/MappingScoringFunction.html de.jstacs.scoringFunctions.MappingScoringFunction] that allows for internal mapping of symbols from the alphabet
* new package [http://www.jstacs.de/api-1.5/de/jstacs/classifier/scoringFunctionBased/sampling/package-summary.html de.jstacs.classifier.scoringFunctionBases.sampling] containing classifiers that sample their parameters by the Metropolis-Hastings algorithm
* new interface [http://www.jstacs.de/api-1.5/de/jstacs/scoringFunctions/SamplingScoringFunction.html de.jstacs.scoringFunctions.SamplingScoringFunction] for [http://www.jstacs.de/api-1.5/de/jstacs/scoringFunctions/NormalizableScoringFunction.html NormalizableScoringFunctions] that can be used in Metropolis-Hastings sampling of parameters
* bugfix in [http://www.jstacs.de/api-1.5/de/jstacs/io/XMLParser.html XMLParser] for cases, where the tag of interest also occurrs within other, nested tags
 
== Jstacs 1.4 (''released December 31, 2010'') ==
* added [http://www.jstacs.de/api-1.5/de/jstacs/data/DinucleotideProperty.html DincleotideProperty] for computing properties like melting temperature, twist, or G/C content
* support for [http://www.jstacs.de/api-1.5/de/jstacs/data/sequences/MultiDimensionalDiscreteSequence.html multidimensional sequence data]
* more widespread use of [http://www.jstacs.de/api-1.5/de/jstacs/algorithms/optimization/termination/TerminationCondition.html TerminationConditions]
* completely rewritten [http://www.jstacs.de/api-1.5/de/jstacs/io/XMLParser.html XMLParser]
* extension of motif discovery to weighted data
* [http://www.jstacs.de/api-1.5/de/jstacs/classifier/scoringFunctionBased/gendismix/OneSampleLogGenDisMixFunction.html OneSampleLogGenDisMixFunction] for using the same Sample with different weights for the different classes
* Jstacs requires Java 1.6 now
 
== Jstacs 1.3.1 (''released March 2, 2010'') ==
* Partitioning of [http://www.jstacs.de/api-1.5/de/jstacs/data/Sample.html Sample]s including weights
* Release of [[Dispom]] (de-novo discovery of differentially abundant transcription factor binding sites including their positional preference)
* Several bugfixes
 
== Jstacs 1.3 (''released December 2, 2009'') ==
* generalized termination of numerical optimization in [http://www.jstacs.de/api-1.5/de/jstacs/algorithms/optimization/termination/package-summary.html de.jstacs.algorithms.optimization.termination]
* Added a unified generative-discriminative learning principle in [http://www.jstacs.de/api-1.5/de/jstacs/classifier/scoringFunctionBased/gendismix/package-summary.html de.jstacs.classifier.scoringFunctionBased.gendismix]
* Implemented a multi-threaded variant of MCL/MSP and GenDisMix in the [http://www.jstacs.de/api-1.5/de/jstacs/classifier/scoringFunctionBased/gendismix/LogGenDisMixFunction.html LogGenDisMixFunction]
* Added a convenience class [http://www.jstacs.de/api-1.5/de/jstacs/data/DNASample.html DNASample] for samples of DNA sequences
* Added the class [http://www.jstacs.de/api-1.5/de/jstacs/parameters/ParameterSetTagger.html ParameterSetTagger] to use parameter sets in command line programs
* Several bugfixes
 
== Jstacs 1.2.2 (''released April 8, 2009'') ==
* Bugfix-Release
 
== Jstacs 1.2.1 (''released February 19, 2009'') ==
* Bugfix in [http://www.jstacs.de/api-1.5/de/jstacs/parameters/EnumParameter.html EnumParameter]
 
== Jstacs 1.2 (''released February 2, 2009'') ==
* Bugfixes
* Discriminative de-novo motif discovery
* [http://www.jstacs.de/api-1.5/de/jstacs/classifier/scoringFunctionBased/logPrior/CompositeLogPrior.html Transformed Dirichlet Prior for numerical optimization]
 
== Jstacs 1.1 (''released October 29, 2008'') ==
* Bugfixes
* Improved Javadoc
* [http://www.jstacs.de/api-1.5/de/jstacs/motifDiscovery/MotifDiscoverer.html De-novo motif discovery]
 
== Jstacs 1.0 (''released September 8, 2008'') ==
The first version of Jstacs has been released.
The first version of Jstacs has been released.

Latest revision as of 16:39, 8 September 2017

This page briefly summarizes the changes in Jstacs. Each release is listed as separate section.

Jstacs 2.3 (released September 8, 2017)

New classes and packages

New features and improvements

  • Alignments may now handle different costs for insert and delete gaps
  • ListResults may now be constructed from Collections of ResultSets
  • Several minor improvements and bugfixes in many classes
  • Improvements of documentation of several classes

Jstacs 2.2 (released February 12, 2016)

New classes and packages

New features and improvements

  • Major restructuring of Alignment for better efficiency
  • Alignment Costs and StringAlignment now Storable
  • New constructor of DataSet allowing a specified percentage of sequences to mismatch the given alphabet
  • BioJavaAdapter ported to BioJava 1.9
  • XMLParser now also allows for storing Sequences
  • New method for parsing HMMer profile HMMs in HMMFactory
  • Several minor improvements and bugfixes in many classes
  • Improvements of documentation of several classes

Jstacs 2.1 (released Mai 31, 2013)

New classes

New features and improvements

Restructuring:

Several minor new features, bug fixes, and code cleanups

Jstacs 2.0 (released February 2, 2012)

Jstacs 2.0 changes many names and the structure of several packages. It is not code-compatible with Jstacs 1.5 and earlier

Restructuring and Renaming

New functionality

Bugfixes/Improvements

Documentation

  • improved Javadocs in many classes and packages
  • new Cookbook with extensive documentation and explanation

Misc

  • output of NonParsableException more verbose
  • Exceptions in multi-threaded code now lead to exit of program instead of only stopping the thread
  • update of RServe/RClient

Jstacs 1.5 (released June 1, 2011)

Jstacs 1.4 (released December 31, 2010)

Jstacs 1.3.1 (released March 2, 2010)

  • Partitioning of Samples including weights
  • Release of Dispom (de-novo discovery of differentially abundant transcription factor binding sites including their positional preference)
  • Several bugfixes

Jstacs 1.3 (released December 2, 2009)

Jstacs 1.2.2 (released April 8, 2009)

  • Bugfix-Release

Jstacs 1.2.1 (released February 19, 2009)

Jstacs 1.2 (released February 2, 2009)

Jstacs 1.1 (released October 29, 2008)

Jstacs 1.0 (released September 8, 2008)

The first version of Jstacs has been released.