edu.msu.cme.rdp.classifier.rrnaclassifier
Class ClassifierCmd

java.lang.Object
  edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierCmd

public class ClassifierCmd
extends java.lang.Object

This is the command line class to do the classification.

Field Summary

private ClassificationResultFormatter.FORMAT	defaultFormat
static java.lang.String	FORMAT_DESC
static java.lang.String	FORMAT_LONG_OPT
static java.lang.String	FORMAT_SHORT_OPT
private static org.apache.commons.cli.Options	options
static java.lang.String	OUTFILE_DESC
static java.lang.String	OUTFILE_LONG_OPT
static java.lang.String	OUTFILE_SHORT_OPT
static java.lang.String	QUERYFILE_DESC
static java.lang.String	QUERYFILE_LONG_OPT
static java.lang.String	QUERYFILE_SHORT_OPT
static java.lang.String	TRAINPROPFILE_DESC
static java.lang.String	TRAINPROPFILE_LONG_OPT
static java.lang.String	TRAINPROPFILE_SHORT_OPT

Constructor Summary

ClassifierCmd()

Method Summary

void	doClassify(java.lang.String inputFile, java.lang.String outFile, java.lang.String propfile, ClassificationResultFormatter.FORMAT format) It classifies query sequences from the input file.
static void	main(java.lang.String[] args) This is the main method to do classification.
static void	printLicense() Prints the license information to std err.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

options

private static org.apache.commons.cli.Options options

QUERYFILE_LONG_OPT

public static final java.lang.String QUERYFILE_LONG_OPT

See Also:

Constant Field Values

OUTFILE_LONG_OPT

public static final java.lang.String OUTFILE_LONG_OPT

See Also:

Constant Field Values

TRAINPROPFILE_LONG_OPT

public static final java.lang.String TRAINPROPFILE_LONG_OPT

See Also:

Constant Field Values

FORMAT_LONG_OPT

public static final java.lang.String FORMAT_LONG_OPT

See Also:

Constant Field Values

QUERYFILE_SHORT_OPT

public static final java.lang.String QUERYFILE_SHORT_OPT

See Also:

Constant Field Values

OUTFILE_SHORT_OPT

public static final java.lang.String OUTFILE_SHORT_OPT

See Also:

Constant Field Values

TRAINPROPFILE_SHORT_OPT

public static final java.lang.String TRAINPROPFILE_SHORT_OPT

See Also:

Constant Field Values

FORMAT_SHORT_OPT

public static final java.lang.String FORMAT_SHORT_OPT

See Also:

Constant Field Values

QUERYFILE_DESC

public static final java.lang.String QUERYFILE_DESC

See Also:

Constant Field Values

OUTFILE_DESC

public static final java.lang.String OUTFILE_DESC

See Also:

Constant Field Values

TRAINPROPFILE_DESC

public static final java.lang.String TRAINPROPFILE_DESC

See Also:

Constant Field Values

FORMAT_DESC

public static final java.lang.String FORMAT_DESC

See Also:

Constant Field Values

defaultFormat

private ClassificationResultFormatter.FORMAT defaultFormat

Constructor Detail

ClassifierCmd

public ClassifierCmd()

Method Detail

doClassify

public void doClassify(java.lang.String inputFile,
                       java.lang.String outFile,
                       java.lang.String propfile,
                       ClassificationResultFormatter.FORMAT format)
                throws java.io.IOException,
                       TrainingDataException,
                       SequenceParserException

It classifies query sequences from the input file. If the property file of the mapping of the training files is not null, the default property file will be override. The classification results will be writen to the output file.

Throws:

java.io.IOException

TrainingDataException

SequenceParserException

printLicense

public static void printLicense()

Prints the license information to std err.

main

public static void main(java.lang.String[] args)
                 throws java.lang.Exception

This is the main method to do classification.

Usage: java ClassifierCmd queryFile outputFile [property file].
queryFile can be one of the following formats: Fasta, Genbank and EMBL.
outputFile will be used to save the classification output.
property file contains the mapping of the training files.
Note: the training files and the property file should be in the same directory. The default property file is set to data/classifier/rRNAClassifier.properties.

Throws:

java.lang.Exception