## Package edu.msu.cme.rdp.classifier.rrnaclassifier

Provides classes for reading training information and classifying sequence.

See:
Description

Class Summary
ClassificationResult: This class holds the classification results for a query sequence.
ClassificationResultFormatter
Classifier: This is the class to do the classification.
ClassifierCmd: This is the command line class to do the classification.
ClassifierFactory: A factory to create a classifier with the training information defined by the property file.
ClassifierTest: A test class for Classifier.
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.
HierarchyTreeTest: A test class for HierarchyTree.
HierarchyVersion: A HierarchyVersion holds the training set number and version of the taxonomy.
LogWordPriorFileParser: A parser to parse a read containing a list of the indices of words and the log value of word prior probabilities.
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.
TrainingInfo: The TrainingInfo holds all the training information and taxonomy hierarchy information.
TrainingInfoTest: A test class for TrainingInfo.
TreeFileParser: A parser to parse a reader containing taxonomic training information.
TreeFileParserTest: A test class for TreeFileParser.

Enum Summary
ClassificationResultFormatter.FORMAT

Exception Summary
ShortSequenceException: Handles exception for a short sequence.
TrainingDataException: Handles the exception occurred when parsing training information.

## Package edu.msu.cme.rdp.classifier.rrnaclassifier Description

Provides classes for reading training information and classifying sequence.

These classes are capable of reading training information from a property file and classifying a sequence. This package contains three main groups of classes:

- Classes for parsing the traing information.
- Classes for sequence classification.
- Classes for holding classification result.