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.