edu.msu.cme.rdp.classifier.comparison
Class ComparisonCmd

java.lang.Object
  edu.msu.cme.rdp.classifier.comparison.ComparisonCmd

public class ComparisonCmd
extends java.lang.Object

Field Summary

static java.lang.String	CLASS_OUTFILE_DESC
static java.lang.String	CLASS_OUTFILE_LONG_OPT
static java.lang.String	CLASS_OUTFILE_SHORT_OPT
static java.lang.String	COMPARE_OUTFILE_DESC
static java.lang.String	COMPARE_OUTFILE_LONG_OPT
static java.lang.String	COMPARE_OUTFILE_SHORT_OPT
static java.lang.String	CONF_DESC
static java.lang.String	CONF_LONG_OPT
static java.lang.String	CONF_SHORT_OPT
private float	confidenceCutoff
static float	DEFAULT_CON_CUTOFF
static ClassificationResultFormatter.FORMAT	DEFAULT_FORMAT
private ClassifierFactory	factory
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	QUERYFILE_DESC
static java.lang.String	QUERYFILE1_LONG_OPT
static java.lang.String	QUERYFILE1_SHORT_OPT
static java.lang.String	QUERYFILE2_LONG_OPT
static java.lang.String	QUERYFILE2_SHORT_OPT
private static java.lang.String	SAMPLE1
private static java.lang.String	SAMPLE2
static java.lang.String	TRAINPROPFILE_DESC
static java.lang.String	TRAINPROPFILE_LONG_OPT
static java.lang.String	TRAINPROPFILE_SHORT_OPT

Constructor Summary

ComparisonCmd(java.lang.String propfile)
Creates a new Manager

Method Summary

void	doClassify(java.lang.String s1, java.lang.String s2, java.lang.String detailFile, java.lang.String sigFile, ClassificationResultFormatter.FORMAT format) given the parser and root, calls the tester to do the classification
static void	main(java.lang.String[] args)
static void	printLicense() Prints the license information to std err.
private void	printSignificance(TaxonTree root, java.io.BufferedWriter wt)
private TaxonTree	reconstructTree(ClassificationResult result, TaxonTree root, java.lang.String sample) reconstruct the hierarchical tree based on the ClassificationResult we assume that the first assignment is always the root and the only root
private void	setConfidenceCutoff(float conf)

Methods inherited from class java.lang.Object

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

Field Detail

QUERYFILE1_LONG_OPT

public static final java.lang.String QUERYFILE1_LONG_OPT

See Also:

Constant Field Values

QUERYFILE2_LONG_OPT

public static final java.lang.String QUERYFILE2_LONG_OPT

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Constant Field Values

CLASS_OUTFILE_LONG_OPT

public static final java.lang.String CLASS_OUTFILE_LONG_OPT

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Constant Field Values

COMPARE_OUTFILE_LONG_OPT

public static final java.lang.String COMPARE_OUTFILE_LONG_OPT

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Constant Field Values

TRAINPROPFILE_LONG_OPT

public static final java.lang.String TRAINPROPFILE_LONG_OPT

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Constant Field Values

FORMAT_LONG_OPT

public static final java.lang.String FORMAT_LONG_OPT

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Constant Field Values

CONF_LONG_OPT

public static final java.lang.String CONF_LONG_OPT

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Constant Field Values

QUERYFILE1_SHORT_OPT

public static final java.lang.String QUERYFILE1_SHORT_OPT

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Constant Field Values

QUERYFILE2_SHORT_OPT

public static final java.lang.String QUERYFILE2_SHORT_OPT

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Constant Field Values

CLASS_OUTFILE_SHORT_OPT

public static final java.lang.String CLASS_OUTFILE_SHORT_OPT

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Constant Field Values

COMPARE_OUTFILE_SHORT_OPT

public static final java.lang.String COMPARE_OUTFILE_SHORT_OPT

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Constant Field Values

TRAINPROPFILE_SHORT_OPT

public static final java.lang.String TRAINPROPFILE_SHORT_OPT

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Constant Field Values

FORMAT_SHORT_OPT

public static final java.lang.String FORMAT_SHORT_OPT

See Also:

Constant Field Values

CONF_SHORT_OPT

public static final java.lang.String CONF_SHORT_OPT

See Also:

Constant Field Values

QUERYFILE_DESC

public static final java.lang.String QUERYFILE_DESC

See Also:

Constant Field Values

CLASS_OUTFILE_DESC

public static final java.lang.String CLASS_OUTFILE_DESC

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Constant Field Values

COMPARE_OUTFILE_DESC

public static final java.lang.String COMPARE_OUTFILE_DESC

See Also:

Constant Field Values

TRAINPROPFILE_DESC

public static final java.lang.String TRAINPROPFILE_DESC

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Constant Field Values

FORMAT_DESC

public static final java.lang.String FORMAT_DESC

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Constant Field Values

CONF_DESC

public static final java.lang.String CONF_DESC

See Also:

Constant Field Values

DEFAULT_CON_CUTOFF

public static final float DEFAULT_CON_CUTOFF

See Also:

Constant Field Values

DEFAULT_FORMAT

public static final ClassificationResultFormatter.FORMAT DEFAULT_FORMAT

options

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

factory

private ClassifierFactory factory

confidenceCutoff

private float confidenceCutoff

SAMPLE1

private static final java.lang.String SAMPLE1

See Also:

Constant Field Values

SAMPLE2

private static final java.lang.String SAMPLE2

See Also:

Constant Field Values

Constructor Detail

ComparisonCmd

public ComparisonCmd(java.lang.String propfile)
              throws java.io.IOException,
                     TrainingDataException

Creates a new Manager

Throws:

java.io.IOException

TrainingDataException

Method Detail

doClassify

public void doClassify(java.lang.String s1,
                       java.lang.String s2,
                       java.lang.String detailFile,
                       java.lang.String sigFile,
                       ClassificationResultFormatter.FORMAT format)
                throws java.io.IOException,
                       SequenceParserException

given the parser and root, calls the tester to do the classification

Throws:

java.io.IOException

SequenceParserException

reconstructTree

private TaxonTree reconstructTree(ClassificationResult result,
                                  TaxonTree root,
                                  java.lang.String sample)

reconstruct the hierarchical tree based on the ClassificationResult we assume that the first assignment is always the root and the only root

printSignificance

private void printSignificance(TaxonTree root,
                               java.io.BufferedWriter wt)
                        throws java.io.IOException

Throws:

java.io.IOException

setConfidenceCutoff

private void setConfidenceCutoff(float conf)

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

Throws:

java.lang.Exception