Version history

Mai 31, 2013:
Jstacs 2.1 released

New classes:

• MultipleIterationsCondition: Requires another TerminationCondition to fail a contiguous, specified number of times
• ClassifierFactory: Allows for creating standard classifiers
• SeqLogoPlotter: Plot PNG sequence logos from within Jstacs
• MultivariateGaussianEmission: Multivariate Gaussian emission density for a Hidden Markov Model
• MEManager: Maximum entropy model

New features and improvements:

• Alignment: Added free shift alignment
• PerformanceMeasure and sub-classes: Extension to weighted test data
• DNAAlphabet: Parser speed-up
• PFMComparator: Extension to PFM from other sources/databases
• ToolBox: New convenience methods for computing several statistics (e.g., median, correlation)
• SignificantMotifOccurrencesFinder: New methods for computing PWMs and statistics from predictions
• SequenceScore and sub-classes: New method toString(NumberFormat)
• AbstractClassifier, ClassifierAssessment and sub-classes: Adaption to weighted PerformanceMeasures
• DataSet: Adaption to weighted data, e.g., partitioning
• REnvironment: Changed several methods from String to CharSequence

Restructuring:

• changed MultiDimensionalSequenceWrapperDiffSM to MultiDimensionalSequenceWrapperDiffSS

Several minor new features, bug fixes, and code cleanups

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February 2, 2012:
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

Restructuring and Renaming:

• former ScoringFunction, NormalizableScoringFunction, Model
  • new base-interface SequenceScore
  • new sub-interface StatisticalModel of SequenceScore for all statistical models with sub-iterfaces DifferentiableStatisticalModel and TrainableStatisticalModel
  • new interface DifferentiableSequenceScore replaces ScoringFunction
  • new interface DifferentiableStatisticalModel replaces NormalizableScoringFunction
  • new interface TrainableStatisticalModel replaces Model
  • new abstract class AbstractDifferentiableSequenceScore
  • new abstract class AbstractDifferentiableStatisticalModel replaces AbstractNormalizableScoringFunction
  • new abstract class 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 DataSet
• Parameters and Results
  • new super-class of Parameters and Results: AnnotatedEntity
  • common list-type for Parameters and Results: AnnotatedEntityList
  • Renaming: CollectionParameter -> SelectionParameter, MultiSelectionCollectionParameter -> MultiSelectionParameter, new super-class AbstractSelectionParameter
  • major refactoring due to common hierarchy and code-cleanup
  • lazy evaluation of Parameter/ParameterSet hierarchies moved from ParameterSet (loadParameters()) to ParameterSetContainer (constructor on class)
  • SubclassFinder adapted to lazy evaluation
• performance measures
  • new abstract super-class AbstractPerformanceMeasure of all performance measures
  • new interface NumericalPerformanceMeasure for all performance measures that return a single number (as opposed, e.g., to curves)
  • new class PerformanceMeasureParameterSet for a collection of general performance measures
  • new class NumericalPerformanceMeasureParameterSet for a collection of NumericalPerformanceMeasures
  • used in evaluate-method of AbstractClassifier and in ClassifierAssessments
• evaluate and evaluateAll in AbstractClassifier joined
• new class IndependentProductDiffSS as super-class of IndepedentProductDiffSM (former IndependentProductScoringFunction)
• new class UniformDiffSS as super-class of UniformDiffSM (former UniformScoringFunction)

New functionality:

• multi-threaded implementation of Baum-Welch and Viterbi training of hidden Markov models
• new Interface Singleton that can be used for singleton instances to save memory, current examples: DNAAlphabet, DNAAlphabetContainer, ProteinAlphabet
• added possibility to use NaN-values with ContinuousAlphabets
• added ProteinAlphabet
• added ArbitraryFloatSequence including static methods for DataSet creation for cases where double-precision is not needed
• new performance measure MaximumFMeasure
• access to Parameters in ParameterSets and Results in ResultSets by name
• emitDataSet in BayesianNetworkDiffSM
• new static method Time.getTimeInstance that returns UserTime or RealTime depending on availability of shared lib
• SubclassFinder allows for adding own base packages
• new method overlaps() in LocatedSequenceAnnotationWithLength
• AbstractTerminationCondition used in ScoreClassifier and sub-classes
• public method propagateESS in HMMFactory
• new method generateLog in DirichletMRG for drawing log-values
• added DifferentiableStatisticalModelFactory

Bugfixes/Improvements:

• bugfix in propagation of equivalent sample size in HMMFactory
• bugfix in random initialization of BasicHigherOrderTransition
• improved Alignment implementation
• 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 NonParsableException more verbose
• Exceptions in multi-threaded code now lead to exit of program instead of only stopping the thread
• update of RServe/RClient

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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.