JavaScript is disabled on your browser.
Overview
Package
Class
Tree
Deprecated
Index
Help
Prev
Next
Frames
No Frames
All Classes
Hierarchy For All Packages
Package Hierarchies:
edu.dartmouth.bglab
,
edu.dartmouth.bglab.beam
,
edu.dartmouth.bglab.beam.web
,
edu.dartmouth.bglab.dataImportPreparation
,
edu.dartmouth.bglab.io
,
edu.dartmouth.bglab.model
,
edu.dartmouth.bglab.motif
,
edu.dartmouth.bglab.score
,
edu.dartmouth.bglab.search
,
edu.dartmouth.bglab.test
,
edu.dartmouth.bglab.util
Class Hierarchy
java.lang.Object
java.util.AbstractMap<K,V> (implements java.util.Map<K,V>)
edu.dartmouth.bglab.util.
SoftValueHashMap
<K,V> (implements java.io.Serializable)
edu.dartmouth.bglab.search.
MotifFinder.FindResultsSoftValueHashMap
edu.dartmouth.bglab.search.
MotifFinder.GenomeSoftValueHashMap
edu.dartmouth.bglab.score.
Scorer.ScoreSoftValueHashMap
edu.dartmouth.bglab.model.
AffinityEvaluator
edu.dartmouth.bglab.model.
AffinityEvaluatorDriver
edu.dartmouth.bglab.model.
AffinityEvaluatorDriver.AffinityFileFilter
(implements java.io.FileFilter)
edu.dartmouth.bglab.model.
AffinityEvaluatorDriver.BackgroundEvalFunc
(implements edu.dartmouth.bglab.model.
AffinityEvaluatorDriver.EvaluatorFunction
)
edu.dartmouth.bglab.model.
AffinityEvaluatorDriver.FPFNEvalFunc
edu.dartmouth.bglab.model.
AffinityEvaluatorDriver.ROCEvalFunc
edu.dartmouth.bglab.model.
AffinityEvaluatorDriver.SiteFileFilter
(implements java.io.FileFilter)
edu.dartmouth.bglab.model.
AffinityEvaluatorDriver.TestModel
edu.dartmouth.bglab.search.
AggregatedFindResults
(implements edu.dartmouth.bglab.search.
FindResults
)
edu.dartmouth.bglab.motif.
Alphabet
edu.dartmouth.bglab.beam.
Ambiguizer
edu.dartmouth.bglab.test.
AmbiguizerTester
edu.dartmouth.bglab.util.
AveStatBox
(implements edu.dartmouth.bglab.util.
StatBox
)
edu.dartmouth.bglab.beam.
BayesDeltaSig
edu.dartmouth.bglab.beam.
Beam
edu.dartmouth.bglab.beam.
BeamDriverFactory
edu.dartmouth.bglab.test.
BeamTester
edu.dartmouth.bglab.util.
Binomial
edu.dartmouth.bglab.beam.
CGIDriver.MotifGeneListSummary
edu.dartmouth.bglab.beam.
CGIDriver.MotifGeneSummary
(implements java.lang.Comparable<T>)
edu.dartmouth.bglab.beam.
CGIScope
edu.dartmouth.bglab.test.
CharlieTester
edu.dartmouth.bglab.search.
CompositeMotifFinder.CompositeFindResults
(implements edu.dartmouth.bglab.search.
FindResults
)
edu.dartmouth.bglab.model.
ConsensusSequence
(implements edu.dartmouth.bglab.model.
CREModel
)
edu.dartmouth.bglab.model.
PLConsensusModel
java.util.Dictionary<K,V>
java.util.Hashtable<K,V> (implements java.lang.Cloneable, java.util.Map<K,V>, java.io.Serializable)
java.util.Properties
edu.dartmouth.bglab.util.
UberProperties
edu.dartmouth.bglab.io.
FileReaders
edu.dartmouth.bglab.io.
FileReaders.NameAndID
(implements java.lang.Comparable<T>)
edu.dartmouth.bglab.io.
FileWriters
edu.dartmouth.bglab.util.
FPFNStatBox
(implements edu.dartmouth.bglab.util.
StatBox
)
edu.dartmouth.bglab.util.
Gaussian
edu.dartmouth.bglab.beam.web.
GeneMapImageDrawer
edu.dartmouth.bglab.beam.web.
GeneMapImageDrawer.Gene
edu.dartmouth.bglab.beam.web.
GeneMapImageDrawer.Motif
edu.dartmouth.bglab.beam.web.
GeneMapImageDrawer.MotifInstance
edu.dartmouth.bglab.dataImportPreparation.
GffToSql
edu.dartmouth.bglab.
GlobalParams
edu.dartmouth.bglab.beam.web.
GraphicsEnvironment
edu.dartmouth.bglab.util.
Heap
edu.dartmouth.bglab.util.
Histogram
edu.dartmouth.bglab.test.
IOTester
edu.dartmouth.bglab.model.
KMismatchModel
(implements edu.dartmouth.bglab.model.
CREModel
)
edu.dartmouth.bglab.model.
KRModel
(implements edu.dartmouth.bglab.util.
Binnable
, java.lang.Comparable<T>, edu.dartmouth.bglab.model.
ProbCREModel
)
edu.dartmouth.bglab.util.
KS
edu.dartmouth.bglab.util.
LinCorrStatBox
(implements edu.dartmouth.bglab.util.
StatBox
)
edu.dartmouth.bglab.util.
LinCorrStatBox.Point
edu.dartmouth.bglab.search.
MarkovModel.KeyComparator
(implements java.util.Comparator<T>)
edu.dartmouth.bglab.score.
MaximalMatcher
edu.dartmouth.bglab.util.
MiscUtils
edu.dartmouth.bglab.model.
ModelEvaluator
edu.dartmouth.bglab.test.
ModelTester
edu.dartmouth.bglab.util.
MoreArrays
edu.dartmouth.bglab.util.
MoreMath
edu.dartmouth.bglab.motif.
Motif
(implements edu.dartmouth.bglab.util.
Binnable
, java.lang.Cloneable, java.lang.Comparable<T>, java.io.Serializable)
edu.dartmouth.bglab.motif.
Motif.LastExpansion
edu.dartmouth.bglab.motif.
Motif.ScoreData
(implements java.lang.Comparable<T>)
edu.dartmouth.bglab.motif.
MotifComparator
(implements java.util.Comparator<T>)
edu.dartmouth.bglab.motif.
ReverseScoreComparator
edu.dartmouth.bglab.motif.
ScoreComparator
edu.dartmouth.bglab.motif.
SequenceComparator
edu.dartmouth.bglab.motif.
EquivalenceComparator
edu.dartmouth.bglab.motif.
OverlapComparator
edu.dartmouth.bglab.score.
PhiComparator
edu.dartmouth.bglab.score.
MotifFilter
edu.dartmouth.bglab.search.
MotifFinder
(implements java.lang.Cloneable, java.io.Serializable)
edu.dartmouth.bglab.search.
ComparatorMotifFinder
edu.dartmouth.bglab.search.
CompositeMotifFinder
edu.dartmouth.bglab.search.
MarkovModel
edu.dartmouth.bglab.search.
SuffixArrayMotifFinder
edu.dartmouth.bglab.search.
MotifFinder.EmptyFindResults
(implements edu.dartmouth.bglab.search.
FindResults
)
edu.dartmouth.bglab.search.
MotifFinder.UncompressedFindResults
(implements edu.dartmouth.bglab.search.
FindResults
, java.io.Serializable)
edu.dartmouth.bglab.search.
MotifFinderFactory
edu.dartmouth.bglab.motif.
MotifInstance
(implements java.lang.Comparable<T>)
edu.dartmouth.bglab.motif.
MotifList
(implements edu.dartmouth.bglab.util.
Binnable
, java.lang.Cloneable, java.lang.Comparable<T>)
edu.dartmouth.bglab.test.
MotifTester
edu.dartmouth.bglab.motif.
MotifUtils
edu.dartmouth.bglab.util.
NiceFormatter
edu.dartmouth.bglab.io.
OrganismLoader
edu.dartmouth.bglab.io.
OrganismLoader.FastaRecord
edu.dartmouth.bglab.beam.
PhiScoreDriver.SuffixFilter
(implements java.io.FilenameFilter)
edu.dartmouth.bglab.util.
Poisson
edu.dartmouth.bglab.util.
Print
edu.dartmouth.bglab.beam.
PRISM
edu.dartmouth.bglab.model.
PWM
(implements edu.dartmouth.bglab.util.
Binnable
, java.lang.Comparable<T>, edu.dartmouth.bglab.model.
ProbCREModel
)
edu.dartmouth.bglab.model.
PWM.StringDoublePair
edu.dartmouth.bglab.model.
PWMEvaluator
edu.dartmouth.bglab.util.
Range
(implements java.lang.Comparable<T>)
edu.dartmouth.bglab.beam.
RankedMotifPair
(implements java.lang.Cloneable, java.lang.Comparable<T>)
edu.dartmouth.bglab.beam.
RankedMotifPair.FoundMotifComparator
(implements java.util.Comparator<T>)
edu.dartmouth.bglab.beam.
ResultsEvaluator
edu.dartmouth.bglab.io.
Scanner
edu.dartmouth.bglab.beam.
Scope
edu.dartmouth.bglab.score.
Scorer
edu.dartmouth.bglab.score.
CombinedScorer
edu.dartmouth.bglab.score.
ConservationRatioScorer
edu.dartmouth.bglab.score.
GroupScorer
edu.dartmouth.bglab.score.
ConservationICScorer
edu.dartmouth.bglab.score.
CoverageScorer
edu.dartmouth.bglab.score.
KSGroupScorer
edu.dartmouth.bglab.score.
OccurrenceKSScorer
edu.dartmouth.bglab.score.
OccurrenceScorer
edu.dartmouth.bglab.score.
LogOccurrenceScorer
edu.dartmouth.bglab.score.
RatioScorer
edu.dartmouth.bglab.score.
RelativeEntropyScorer
edu.dartmouth.bglab.score.
KSScorer
edu.dartmouth.bglab.score.
MarkovMaxOrderScorer
edu.dartmouth.bglab.score.
ZScoreScorer
edu.dartmouth.bglab.score.
ScorerFactory
edu.dartmouth.bglab.test.
ScoreTester
edu.dartmouth.bglab.test.
SearchTester
edu.dartmouth.bglab.search.
SearchUtils
edu.dartmouth.bglab.beam.web.
ServerSocketImageWriter.Gene
edu.dartmouth.bglab.beam.web.
ServerSocketImageWriter.Motif
edu.dartmouth.bglab.beam.web.
ServerSocketImageWriter.MotifInstance
edu.dartmouth.bglab.util.
Stopwatch
edu.dartmouth.bglab.util.
SuffixArray
edu.dartmouth.bglab.search.
SuffixArrayMotifFinder.SuffixArrayFindResults
(implements java.lang.Comparable<T>, edu.dartmouth.bglab.search.
FindResults
)
edu.dartmouth.bglab.io.
SynonymChecker
edu.dartmouth.bglab.io.
SynonymLoader
java.lang.Thread (implements java.lang.Runnable)
edu.dartmouth.bglab.beam.
BeamDriver
edu.dartmouth.bglab.beam.
AssessmentDriver
edu.dartmouth.bglab.beam.
BackgroundDriver
edu.dartmouth.bglab.beam.
BiologicalBeamDriver
edu.dartmouth.bglab.beam.
CGIDriver
edu.dartmouth.bglab.beam.
CorruptionDriver
edu.dartmouth.bglab.beam.
FASTAdriver
edu.dartmouth.bglab.beam.
LinearityTesterDriver
edu.dartmouth.bglab.beam.
MLDriver
edu.dartmouth.bglab.beam.
PhiScoreDriver
edu.dartmouth.bglab.beam.
ScoreDriver
edu.dartmouth.bglab.beam.
ScoreKnownsDriver
edu.dartmouth.bglab.beam.web.
WebDriver
edu.dartmouth.bglab.beam.web.
WebDriverJr
edu.dartmouth.bglab.beam.web.
ServerSocketImageWriter
edu.dartmouth.bglab.beam.web.
StreamPipe
edu.dartmouth.bglab.util.
ThreadDriver
java.lang.Throwable (implements java.io.Serializable)
edu.dartmouth.bglab.beam.web.
ChildProcessProblem
java.lang.Exception
edu.dartmouth.bglab.model.
ExpansionTooLargeException
java.lang.RuntimeException
edu.dartmouth.bglab.io.
IllegalFastaFileException
edu.dartmouth.bglab.beam.web.
InvalidGeneListException
edu.dartmouth.bglab.beam.web.
PrematureDeathException
edu.dartmouth.bglab.motif.
UnknownBaseException
edu.dartmouth.bglab.search.
UnsearchableMotifException
edu.dartmouth.bglab.io.
UnknownGeneException
edu.dartmouth.bglab.test.
UtilTester
edu.dartmouth.bglab.beam.
WebScope
Interface Hierarchy
edu.dartmouth.bglab.model.
AffinityEvaluatorDriver.EvaluatorFunction
edu.dartmouth.bglab.util.
Binnable
edu.dartmouth.bglab.util.
StatBox
edu.dartmouth.bglab.util.
CDF
edu.dartmouth.bglab.model.
CREModel
edu.dartmouth.bglab.model.
ProbCREModel
java.io.Serializable
edu.dartmouth.bglab.search.
FindResults
Overview
Package
Class
Tree
Deprecated
Index
Help
Prev
Next
Frames
No Frames
All Classes