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=== New classes and packages ===
=== New classes and packages ===
* CorreationCoefficient PerformanceMeasure
* [http://www.jstacs.de/api-2.2/de/jstacs/classifiers/performanceMeasures/CorrelationCoefficient.html CorreationCoefficient] PerformanceMeasure
* clustering package with classes for hierarchical clustering
* [http://www.jstacs.de/api-2.2/de/jstacs/clustering/hierachical/package-summary.html de.jstacs.clustering] package with classes for hierarchical clustering
* DeBruijnGraphSequenceGenerator and DeBruijnSequenceGenerator for generating De Buijn sequences
* [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
* CyclicSequenceAdaptor for representing cyclic sequences
* [http://www.jstacs.de/api-2.2/de/jstacs/data/sequences/CyclicSequenceAdaptor.html CyclicSequenceAdaptor] for representing cyclic sequences
* PlotGeneratorResult for representing results that plot images to a Graphics2D object
* [http://www.jstacs.de/api-2.2/de/jstacs/results/PlotGeneratorResult.html PlotGeneratorResult] for representing results that plot images to a Graphics2D object
* TextResult for results that may be stored as text files
* [http://www.jstacs.de/api-2.2/de/jstacs/results/TextResult.html TextResult] for results that may be stored as text files
* package results.savers for generic classes that store results to disk
* 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
* LimitedSparseLocalInhomogeneousMixtureDiffSM_higherOrder for sparse local inhomogeneous mixture (Slim) models
* [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
* PFMWrapperTrainSM for representing position frequency matrices and position weight matrices from databases
* [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 de.jstacs.tools with classes for generic Jstacs tools that may be used in different user interfaces (command line, Galaxy, JavaFX)
* 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 (command line, Galaxy, JavaFX)
* Compression for ZIP compression of Strings
* [http://www.jstacs.de/api-2.2/de/jstacs/utils/Compression.html Compression] for ZIP compression of Strings
* package utils.graphics with generic GraphicsAdaptor using Apache XML commons
* 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
* projects: Dimont, GeMoMa, Slim, TALEN, motif comparison


=== New features and improvements ===
=== New features and improvements ===


* Major restructuring of Alignment for better efficiency
* Major restructuring of [http://www.jstacs.de/api-2.2/de/jstacs/algorithms/alignment/Alignment.html Alignment] for better efficiency
* Alignment Costs and StringAlignment now Storable
* 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 DataSet allowing a specified percentage of sequences to mismatch the given alphabet
* 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
* BioJavaAdapter ported to BioJava 1.9
* [http://www.jstacs.de/api-2.2/de/jstacs/data/bioJava/BioJavaAdapter.html BioJavaAdapter] ported to BioJava 1.9
* XMLParser now also allows for storing Sequences
* [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 HMMFactory
* 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
* Several minor improvements and bugfixes in many classes
* Improvements of documentation of several classes
* Improvements of documentation of several classes

Revision as of 16:00, 12 February 2016

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

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.