# All Classes and Interfaces

Class
Description
AbstractNode
BoxPlotUtils
ClassificationParser
ClassificationResult
This class holds the classification results for a query sequence.
ClassificationResultFormatter
ClassificationResultFormatter.FORMAT
Classifier
This is the class to do the classification.
ClassifierCmd
This is the legacy command line class to do the classification.
ClassifierFactory
A factory to create a classifier with the training information defined by the property file.
ClassifierGridware
ClassifierMain
ClassifierSequence
A Sequence containing the sequence information.
ClassifierTraineeMaker
A command line class to create training information from the raw data.
ClassifierTreeBuilder<E>
ClassifierTreeBuilder.ClassifierTaxonFactory<E>
CmdOptions
CompareMisclassified
CompareTrainingSets
ComparisonBrowserBean
ComparisonBrowserNode
ComparisonCmd
ComparisonResultTreeSet
ComparisonResultTreeSet.ComparisonResultComparator
CopyNumberParser
CorrectAssignment
CrossValidate
CrossValidateMain
DecisionMaker
DefaultPrintVisitor
EstimateSPrintVisitor
FindWindowFrame
GenusWordConditionalProb
A GenusWordConditionalProb holds the index of the genus node, and the conditional probability that genus node contains the word.
GenusWordProbFileParser
A parser to parse a reader containing a list of the indices of genus nodes and the conditional probabilities that genus nodes contains the words.
HierarchyTree
A HierarchyTree holds the taxonomic information of a taxon.
HierarchyTree
HierarchyVersion
A HierarchyVersion holds the training set number and version of the taxonomy.
LeaveOneOutTester
LeaveOneOutTesterMain
LineageSequence
A ParsedRawSequence holds the data for a raw sequence.
LineageSequenceParser
A parser to parse a reader containing the raw sequences.
LogWordPriorFileParser
A parser to parse a read containing a list of the indices of words and the log value of word prior probabilities.
Main
MainMovingWindow
MCSample
MCSamplePrintUtil
MCSampleResult
MCTaxon
MergeTaxonCount
MultiClassifier
MultiClassifierResult
NameRankDupException
NBClassifier
PairwiseSeqDistance
PixelCalculatorBean
ProbIndexFileParser
A parser to parser a reader contains a list of indices of words, and start indices of the conditional probabilities.
RankAssignment
A RankAssignment holds the classification result of a sequence at one rank level.
RawGenusWordConditionalProb
A RawGenusWordConditionalProb contains the index of the genus node and the conditional probability of the node contains the word.
RawHierarchyTree
A RawHierarchyTree holds the raw taxon and sequences information.
RdmSelectTaxon
Reprocess
Score
SeqErrorBean
SeqInfo
ShortSequenceException
Handles exception for a short sequence.
SigCalculator
SortedROCSet
SortedROCSet.PredictionCount
SortedROCSet.ResultComparator
StatusCount
StatusCountUtils
TaxaSimilarityMain
Taxon
Taxonomy
A Taxonomy holds the raw taxon information.
Taxonomy
TaxonTree
TrainingDataException
Handles the exception occurred when parsing training information.
TrainingInfo
The TrainingInfo holds all the training information and taxonomy hierarchy information.
TreeFactory
A TreeFactory reads the raw taxonomic information and creates the RawHierarchyTree nodes.
TreeFactory
TreeFileParser
A parser to parse a reader containing taxonomic training information.
UncNode
Unifrac
UnifracTaxon
UnifracTree
UnifracTree.UnifracResult
UnifracTreeBuilder
UnifracTreeBuilder.UnifracSample
ValidationClassificationResult
ValidClassificationResultFacade
Window
WindowTester
Ztable