Version history

June 1, 2011:
Jstacs 1.5 released

• new package de.jstacs.algorithms.alignment for sequence alignment algorithms
• new class de.jstacs.models.ModelFactory with static classes to construct many standard models
• de.jstacs.utils.galaxy.GalaxyAdaptor, an adaptor to Galaxy, which allows for creating Galaxy applications using Jstacs ParameterSets, also requires new interface GalaxyConvertible
• new package 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 de.jstacs.sampling that contains general infrastructure for parameter sampling
• new class de.jstacs.scoringFunctions.MappingScoringFunction that allows for internal mapping of symbols from the alphabet
• new package de.jstacs.classifier.scoringFunctionBases.sampling containing classifiers that sample their parameters by the Metropolis-Hastings algorithm
• new interface de.jstacs.scoringFunctions.SamplingScoringFunction for NormalizableScoringFunctions that can be used in Metropolis-Hastings sampling of parameters
• bugfix in XMLParser for cases, where the tag of interest also occurrs within other, nested tags

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December 31, 2010:
Jstacs 1.4 released

• added DincleotideProperty for computing properties like melting temperature, twist, or G/C content
• support for multidimensional sequence data
• more widespread use of TerminationConditions
• completely rewritten XMLParser
• extension of motif discovery to weighted data
• OneSampleLogGenDisMixFunction for using the same Sample with different weights for the different classes
• Jstacs requires Java 1.6 now

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March 2, 2010:
Jstacs 1.3.1 released

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

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December 2, 2009:
Jstacs 1.3 released

• generalized termination of numerical optimization in de.jstacs.algorithms.optimization.termination
• Added a unified generative-discriminative learning principle in de.jstacs.classifier.scoringFunctionBased.gendismix
• Implemented a multi-threaded variant of MCL/MSP and GenDisMix in the LogGenDisMixFunction
• Added a convenience class DNASample for samples of DNA sequences
• Added the class ParameterSetTagger to use parameter sets in command line programs
• Several bugfixes

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April 8, 2009:
Jstacs 1.2.2 released

• Bugfix-Release

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February 19, 2009:
Jstacs 1.2.1 released

• Bugfix in EnumParameter

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February 2, 2009:
Jstacs 1.2 released

• Bugfixes
• Discriminative de-novo motif discovery
• Transformed Dirichlet Prior for numerical optimization

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October 29, 2008:
Jstacs 1.1 released

• Bugfixes
• Improved Javadoc
• De-novo motif discovery

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September 8, 2008:
The first version of Jstacs has been released.