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''Mai 31, 2013:<br />
This page briefly summarizes the changes in Jstacs. Each release is listed as separate section.
Jstacs 2.1 released


New classes:
== 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/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/classifiers/ClassifierFactory.html ClassifierFactory]: Allows for creating standard classifiers
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* [http://www.jstacs.de/api-2.1/de/jstacs/sequenceScores/statisticalModels/trainable/discrete/inhomogeneous/MEManager.html MEManager]: Maximum entropy 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:
=== 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/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/classifiers/performanceMeasures/PerformanceMeasure.html PerformanceMeasure] and sub-classes: Extension to weighted test data
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* [http://www.jstacs.de/api-2.1/de/jstacs/utils/REnvironment.html REnvironment]: Changed several methods from String to CharSequence
* [http://www.jstacs.de/api-2.1/de/jstacs/utils/REnvironment.html REnvironment]: Changed several methods from String to CharSequence


Restructuring:
=== Restructuring: ===
* changed MultiDimensionalSequenceWrapperDiffSM to [http://www.jstacs.de/api-2.1/de/jstacs/sequenceScores/differentiable/MultiDimensionalSequenceWrapperDiffSS.html MultiDimensionalSequenceWrapperDiffSS]
* 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
Several minor new features, bug fixes, and code cleanups


----
== Jstacs 2.0 (''released February 2, 2012'')==
 
''February 2, 2012:<br />
Jstacs 2.0 released


''Jstacs 2.0 changes many names and the structure of several packages. It is not code-compatible with Jstacs 1.5 and earlier''
''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:
=== Restructuring and Renaming ===
* former ScoringFunction, NormalizableScoringFunction, Model
* former ScoringFunction, NormalizableScoringFunction, Model
** new base-interface [http://www.jstacs.de/api-2.0/de/jstacs/sequenceScores/SequenceScore.html SequenceScore]
** new base-interface [http://www.jstacs.de/api-2.0/de/jstacs/sequenceScores/SequenceScore.html SequenceScore]
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* 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 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:
=== New functionality ===
* multi-threaded implementation of Baum-Welch and Viterbi training of hidden Markov models
* 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]
* 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]
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* added [http://www.jstacs.de/api-2.0/de/jstacs/sequenceScores/statisticalModels/differentiable/DifferentiableStatisticalModelFactory.html DifferentiableStatisticalModelFactory]
* added [http://www.jstacs.de/api-2.0/de/jstacs/sequenceScores/statisticalModels/differentiable/DifferentiableStatisticalModelFactory.html DifferentiableStatisticalModelFactory]


Bugfixes/Improvements:
=== 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 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]
* bugfix in random initialization of [http://www.jstacs.de/api-2.0/de/jstacs/sequenceScores/statisticalModels/trainable/hmm/transitions/BasicHigherOrderTransition.html BasicHigherOrderTransition]
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* [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
* [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:
=== Documentation ===
* improved Javadocs in many classes and packages
* improved Javadocs in many classes and packages
* new [[Cookbook]] with extensive documentation and explanation
* new [[Cookbook]] with extensive documentation and explanation


Misc:
=== Misc ===
* output of [http://www.jstacs.de/api-2.0/de/jstacs/io/NonParsableException.html NonParsableException] more verbose
* 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
* Exceptions in multi-threaded code now lead to exit of program instead of only stopping the thread
* update of RServe/RClient
* update of RServe/RClient


----
== Jstacs 1.5 (''released June 1, 2011'') ==


''June 1, 2011:<br />
Jstacs 1.5 released
* 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 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
* 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
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* 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
* 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'') ==
 
''December 31, 2010:<br />
Jstacs 1.4 released
* 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
* 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]
* support for [http://www.jstacs.de/api-1.5/de/jstacs/data/sequences/MultiDimensionalDiscreteSequence.html multidimensional sequence data]
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* Jstacs requires Java 1.6 now
* Jstacs requires Java 1.6 now


----
== Jstacs 1.3.1 (''released March 2, 2010'') ==
 
''March 2, 2010:<br />
Jstacs 1.3.1 released
* Partitioning of [http://www.jstacs.de/api-1.5/de/jstacs/data/Sample.html Sample]s including weights
* 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)
* Release of [[Dispom]] (de-novo discovery of differentially abundant transcription factor binding sites including their positional preference)
* Several bugfixes
* Several bugfixes


----
== Jstacs 1.3 (''released December 2, 2009'') ==
 
''December 2, 2009:<br />
Jstacs 1.3 released
* 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]
* 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]
* 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]
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* Several bugfixes
* Several bugfixes


----
== Jstacs 1.2.2 (''released April 8, 2009'') ==
 
''April 8, 2009:<br />
Jstacs 1.2.2 released
* Bugfix-Release
* Bugfix-Release


----
== Jstacs 1.2.1 (''released February 19, 2009'') ==
 
''February 19, 2009:<br />
Jstacs 1.2.1 released
* Bugfix in [http://www.jstacs.de/api-1.5/de/jstacs/parameters/EnumParameter.html EnumParameter]
* Bugfix in [http://www.jstacs.de/api-1.5/de/jstacs/parameters/EnumParameter.html EnumParameter]


----
== Jstacs 1.2 (''released February 2, 2009'') ==
 
''February 2, 2009'':<br />
Jstacs 1.2 released
* Bugfixes
* Bugfixes
* Discriminative de-novo motif discovery
* 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]
* [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'') ==
 
''October 29, 2008'':<br />
Jstacs 1.1 released
* Bugfixes
* Bugfixes
* Improved Javadoc
* Improved Javadoc
* [http://www.jstacs.de/api-1.5/de/jstacs/motifDiscovery/MotifDiscoverer.html De-novo motif discovery]
* [http://www.jstacs.de/api-1.5/de/jstacs/motifDiscovery/MotifDiscoverer.html De-novo motif discovery]


----
== Jstacs 1.0 (''released September 8, 2008'') ==
 
''September 8, 2008'':<br />
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.