All Classes and Interfaces
Class
Description
This class holds the classification results for a query sequence.
This is the class to do the classification.
This is the legacy command line class to do the classification.
A factory to create a classifier with the training information defined by the property file.
A Sequence containing the sequence information.
A command line class to create training information from the raw data.
ClassifierTreeBuilder<E extends edu.msu.cme.rdp.taxatree.Taxon>
ClassifierTreeBuilder.ClassifierTaxonFactory<E extends edu.msu.cme.rdp.taxatree.Taxon>
A GenusWordConditionalProb holds the index of the genus node,
and the conditional probability that genus node contains the word.
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.
A HierarchyTree holds the taxonomic information of a taxon.
A HierarchyVersion holds the training set number and version of the taxonomy.
A ParsedRawSequence holds the data for a raw sequence.
A parser to parse a reader containing the raw sequences.
A parser to parse a read containing a list of the indices of words
and the log value of word prior probabilities.
A parser to parser a reader contains a list of indices of words,
and start indices of the conditional probabilities.
A RankAssignment holds the classification result of a sequence at one rank level.
A RawGenusWordConditionalProb contains the index of the genus node and
the conditional probability of the node contains the word.
A RawHierarchyTree holds the raw taxon and sequences information.
Handles exception for a short sequence.
A Taxonomy holds the raw taxon information.
Handles the exception occurred when parsing training information.
The TrainingInfo holds all the training information and taxonomy hierarchy information.
A TreeFactory reads the raw taxonomic information and creates the RawHierarchyTree nodes.
A parser to parse a reader containing taxonomic training information.