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Logo JMLR Jstacs 2.1

by keili - June 3, 2013, 07:32:55 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 13271 views, 3108 downloads, 2 subscriptions

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

Changes:

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
  • AbstractClassifier, ClassifierAssessment and sub-classes: Adaption to weighted PerformanceMeasures
  • 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)
  • 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