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Package Hierarchies:
edu.msu.cme.rdp.classifier
,
edu.msu.cme.rdp.classifier.cli
,
edu.msu.cme.rdp.classifier.comparison
,
edu.msu.cme.rdp.classifier.io
,
edu.msu.cme.rdp.classifier.rrnaclassifier
,
edu.msu.cme.rdp.classifier.train
,
edu.msu.cme.rdp.classifier.train.validation
,
edu.msu.cme.rdp.classifier.train.validation.crossvalidate
,
edu.msu.cme.rdp.classifier.train.validation.distance
,
edu.msu.cme.rdp.classifier.train.validation.leaveoneout
,
edu.msu.cme.rdp.classifier.train.validation.movingwindow
,
edu.msu.cme.rdp.classifier.utils
,
edu.msu.cme.rdp.multicompare
,
edu.msu.cme.rdp.multicompare.gridware
,
edu.msu.cme.rdp.multicompare.taxon
,
edu.msu.cme.rdp.multicompare.visitors
,
edu.msu.cme.rdp.taxatree
,
edu.msu.cme.rdp.taxatree.utils
,
edu.msu.cme.rdp.unifrac
Class Hierarchy
java.lang.Object
java.util.AbstractCollection<E> (implements java.util.Collection<E>)
java.util.AbstractSet<E> (implements java.util.Set<E>)
java.util.TreeSet<E> (implements java.lang.Cloneable, java.util.NavigableSet<E>, java.io.Serializable)
edu.msu.cme.rdp.classifier.comparison.
ComparisonResultTreeSet
edu.msu.cme.rdp.classifier.train.validation.
SortedROCSet
edu.msu.cme.rdp.classifier.comparison.
AbstractNode
(implements edu.msu.cme.rdp.classifier.comparison.
ComparisonBrowserNode
, edu.msu.cme.rdp.classifier.comparison.
Taxon
)
edu.msu.cme.rdp.classifier.comparison.
TaxonTree
edu.msu.cme.rdp.classifier.comparison.
UncNode
edu.msu.cme.rdp.classifier.train.validation.distance.
BoxPlotUtils
edu.msu.cme.rdp.classifier.rrnaclassifier.
ClassificationParser
edu.msu.cme.rdp.classifier.
ClassificationResult
edu.msu.cme.rdp.classifier.io.
ClassificationResultFormatter
edu.msu.cme.rdp.classifier.
Classifier
edu.msu.cme.rdp.classifier.
ClassifierCmd
edu.msu.cme.rdp.classifier.utils.
ClassifierFactory
edu.msu.cme.rdp.multicompare.gridware.
ClassifierGridware
edu.msu.cme.rdp.classifier.cli.
ClassifierMain
edu.msu.cme.rdp.classifier.train.
ClassifierTraineeMaker
edu.msu.cme.rdp.taxatree.utils.
ClassifierTreeBuilder
<E>
edu.msu.cme.rdp.classifier.cli.
CmdOptions
edu.msu.cme.rdp.classifier.train.validation.leaveoneout.
CompareMisclassified
edu.msu.cme.rdp.classifier.train.validation.distance.
CompareTrainingSets
edu.msu.cme.rdp.classifier.train.validation.distance.
CompareTrainingSets.HierarchyTreeExtend
edu.msu.cme.rdp.classifier.comparison.
ComparisonBrowserBean
edu.msu.cme.rdp.classifier.comparison.
ComparisonCmd
edu.msu.cme.rdp.classifier.comparison.
ComparisonResultTreeSet.ComparisonResultComparator
(implements java.util.Comparator<T>)
edu.msu.cme.rdp.taxatree.ConcretRoot<E>
edu.msu.cme.rdp.taxatree.
UnifracTree
edu.msu.cme.rdp.classifier.train.
CopyNumberParser
edu.msu.cme.rdp.classifier.train.
CopyNumberParser.TaxonCopyNumber
edu.msu.cme.rdp.classifier.train.validation.
CorrectAssignment
edu.msu.cme.rdp.classifier.train.validation.crossvalidate.
CrossValidate
edu.msu.cme.rdp.classifier.train.validation.crossvalidate.
CrossValidateMain
edu.msu.cme.rdp.classifier.train.validation.
DecisionMaker
org.xml.sax.helpers.DefaultHandler (implements org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler)
edu.msu.cme.rdp.classifier.io.
TreeFileParser
edu.msu.cme.rdp.multicompare.visitors.
DefaultPrintVisitor
(implements edu.msu.cme.rdp.taxatree.interfaces.TreeVisitor<E>)
edu.msu.cme.rdp.multicompare.visitors.
EstimateSPrintVisitor
(implements edu.msu.cme.rdp.taxatree.interfaces.TreeVisitor<E>)
edu.msu.cme.rdp.classifier.train.validation.movingwindow.
FindWindowFrame
edu.msu.cme.rdp.classifier.
GenusWordConditionalProb
edu.msu.cme.rdp.classifier.io.
GenusWordProbFileParser
edu.msu.cme.rdp.classifier.train.validation.
HierarchyTree
edu.msu.cme.rdp.classifier.
HierarchyTree
edu.msu.cme.rdp.classifier.utils.
HierarchyVersion
edu.msu.cme.rdp.classifier.train.validation.leaveoneout.
LeaveOneOutTester
edu.msu.cme.rdp.classifier.train.validation.leaveoneout.
LeaveOneOutTesterMain
edu.msu.cme.rdp.classifier.train.
LineageSequenceParser
edu.msu.cme.rdp.classifier.io.
LogWordPriorFileParser
edu.msu.cme.rdp.multicompare.
Main
edu.msu.cme.rdp.classifier.train.validation.movingwindow.
MainMovingWindow
edu.msu.cme.rdp.multicompare.
MCSample
edu.msu.cme.rdp.multicompare.
MCSampleResult
edu.msu.cme.rdp.multicompare.
MCSamplePrintUtil
edu.msu.cme.rdp.multicompare.
MergeTaxonCount
edu.msu.cme.rdp.multicompare.
MultiClassifier
edu.msu.cme.rdp.multicompare.
MultiClassifierResult
edu.msu.cme.rdp.classifier.train.validation.
NBClassifier
edu.msu.cme.rdp.taxatree.Node
edu.msu.cme.rdp.taxatree.Taxon
edu.msu.cme.rdp.multicompare.taxon.
MCTaxon
edu.msu.cme.rdp.unifrac.
UnifracTaxon
edu.msu.cme.rdp.classifier.train.validation.distance.
PairwiseSeqDistance
edu.msu.cme.rdp.classifier.comparison.
PixelCalculatorBean
edu.msu.cme.rdp.classifier.io.
ProbIndexFileParser
edu.msu.cme.rdp.classifier.
RankAssignment
edu.msu.cme.rdp.classifier.train.
RawGenusWordConditionalProb
edu.msu.cme.rdp.classifier.train.
RawHierarchyTree
edu.msu.cme.rdp.classifier.train.validation.crossvalidate.
RdmSelectTaxon
edu.msu.cme.rdp.multicompare.
Reprocess
edu.msu.cme.rdp.classifier.comparison.
Score
edu.msu.cme.rdp.classifier.comparison.
SeqErrorBean
edu.msu.cme.rdp.classifier.comparison.
SeqInfo
edu.msu.cme.rdp.readseq.readers.Sequence (implements java.io.Serializable)
edu.msu.cme.rdp.classifier.utils.
ClassifierSequence
edu.msu.cme.rdp.classifier.train.
LineageSequence
edu.msu.cme.rdp.classifier.comparison.
SigCalculator
edu.msu.cme.rdp.classifier.train.validation.
SortedROCSet.PredictionCount
edu.msu.cme.rdp.classifier.train.validation.
SortedROCSet.ResultComparator
(implements java.util.Comparator<T>)
edu.msu.cme.rdp.classifier.train.validation.
StatusCount
edu.msu.cme.rdp.classifier.train.validation.
StatusCountUtils
edu.msu.cme.rdp.classifier.train.validation.distance.
TaxaSimilarityMain
edu.msu.cme.rdp.classifier.train.validation.
Taxonomy
edu.msu.cme.rdp.classifier.train.
Taxonomy
java.lang.Throwable (implements java.io.Serializable)
java.lang.Exception
edu.msu.cme.rdp.classifier.train.
NameRankDupException
java.lang.RuntimeException
java.lang.IllegalArgumentException
edu.msu.cme.rdp.classifier.
ShortSequenceException
edu.msu.cme.rdp.classifier.
TrainingDataException
edu.msu.cme.rdp.classifier.
TrainingInfo
edu.msu.cme.rdp.classifier.train.validation.
TreeFactory
edu.msu.cme.rdp.classifier.train.
TreeFactory
edu.msu.cme.rdp.unifrac.
Unifrac
edu.msu.cme.rdp.taxatree.
UnifracTree.UnifracResult
edu.msu.cme.rdp.unifrac.
UnifracTreeBuilder
edu.msu.cme.rdp.unifrac.
UnifracTreeBuilder.UnifracSample
edu.msu.cme.rdp.classifier.train.validation.
ValidationClassificationResult
edu.msu.cme.rdp.classifier.train.validation.
ValidClassificationResultFacade
edu.msu.cme.rdp.classifier.train.validation.movingwindow.
Window
edu.msu.cme.rdp.classifier.train.validation.movingwindow.
WindowTester
edu.msu.cme.rdp.classifier.comparison.
Ztable
Interface Hierarchy
edu.msu.cme.rdp.taxatree.utils.
ClassifierTreeBuilder.ClassifierTaxonFactory
<E>
edu.msu.cme.rdp.classifier.comparison.
ComparisonBrowserNode
edu.msu.cme.rdp.classifier.comparison.
Taxon
Enum Hierarchy
java.lang.Object
java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
edu.msu.cme.rdp.classifier.io.
ClassificationResultFormatter.FORMAT
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