All Classes
AffinityEvaluator
AffinityEvaluatorDriver
AffinityEvaluatorDriver.AffinityFileFilter
AffinityEvaluatorDriver.BackgroundEvalFunc
AffinityEvaluatorDriver.EvaluatorFunction
AffinityEvaluatorDriver.FPFNEvalFunc
AffinityEvaluatorDriver.ROCEvalFunc
AffinityEvaluatorDriver.SiteFileFilter
AffinityEvaluatorDriver.TestModel
AggregatedFindResults
Alphabet
Ambiguizer
AmbiguizerTester
AssessmentDriver
AveStatBox
BackgroundDriver
BayesDeltaSig
Beam
BeamDriver
BeamDriverFactory
BeamTester
Binnable
Binomial
BiologicalBeamDriver
CDF
CGIDriver
CGIDriver.MotifGeneSummary
CGIScope
CharlieTester
ChildProcessProblem
CombinedScorer
ComparatorMotifFinder
CompositeMotifFinder
CompositeMotifFinder.CompositeFindResults
ConsensusSequence
ConservationICScorer
ConservationRatioScorer
CorruptionDriver
CoverageScorer
CREModel
EquivalenceComparator
ExpansionTooLargeException
FASTAdriver
FileReaders
FileReaders.NameAndID
FileWriters
FindResults
FPFNStatBox
Gaussian
GeneMapImageDrawer
GeneMapImageDrawer.Gene
GeneMapImageDrawer.Motif
GeneMapImageDrawer.MotifInstance
GffToSql
GlobalParams
GraphicsEnvironment
GroupScorer
Heap
Histogram
IllegalFastaFileException
InvalidGeneListException
IOTester
KMismatchModel
KRModel
KS
KSGroupScorer
KSScorer
LinCorrStatBox
LinearityTesterDriver
LogOccurrenceScorer
MarkovMaxOrderScorer
MarkovModel
MarkovModel.KeyComparator
MaximalMatcher
MiscUtils
MLDriver
ModelEvaluator
ModelTester
MoreArrays
MoreMath
Motif
Motif.LastExpansion
Motif.ScoreData
MotifComparator
MotifFilter
MotifFinder
MotifFinder.EmptyFindResults
MotifFinder.FindResultsSoftValueHashMap
MotifFinder.GenomeSoftValueHashMap
MotifFinder.UncompressedFindResults
MotifFinderFactory
MotifInstance
MotifList
MotifTester
MotifUtils
NiceFormatter
OccurrenceKSScorer
OccurrenceScorer
OrganismLoader
OrganismLoader.FastaRecord
OverlapComparator
PhiComparator
PhiScoreDriver
PLConsensusModel
Poisson
PrematureDeathException
Print
PRISM
ProbCREModel
PWM
PWMEvaluator
Range
RankedMotifPair
RankedMotifPair.FoundMotifComparator
RatioScorer
RelativeEntropyScorer
ResultsEvaluator
ReverseScoreComparator
Scanner
Scope
ScoreComparator
ScoreDriver
ScoreKnownsDriver
Scorer
ScorerFactory
ScoreTester
SearchTester
SearchUtils
SequenceComparator
ServerSocketImageWriter
ServerSocketImageWriter.Gene
ServerSocketImageWriter.Motif
ServerSocketImageWriter.MotifInstance
SoftValueHashMap
StatBox
Stopwatch
StreamPipe
SuffixArray
SuffixArrayMotifFinder
SuffixArrayMotifFinder.SuffixArrayFindResults
SynonymChecker
SynonymLoader
ThreadDriver
UberProperties
UnknownBaseException
UnknownGeneException
UnsearchableMotifException
UtilTester
WebDriver
WebDriverJr
WebScope
ZScoreScorer