About: A Java framework for statistical analysis and classification of biological sequences

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()

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

further changes

• Sample renamed to DataSet
• 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 ProteinAlphabet
• added possibility to use NaN-values with ContinuousAlphabets
• 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