Package edu.msu.cme.rdp.classifier.cli

Class CmdOptions

java.lang.Object

edu.msu.cme.rdp.classifier.cli.CmdOptions

public class CmdOptions
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String	BIOMFILE_DESC
static java.lang.String	BIOMFILE_LONG_OPT
static java.lang.String	BIOMFILE_SHORT_OPT
static java.lang.String	BOOTSTRAP_DESC
static java.lang.String	BOOTSTRAP_LONG_OPT
static java.lang.String	BOOTSTRAP_OUTFILE_DESC
static java.lang.String	BOOTSTRAP_OUTFILE_LONG_OPT
static java.lang.String	BOOTSTRAP_OUTFILE_SHORT_OPT
static java.lang.String	BOOTSTRAP_SHORT_OPT
static float	DEFAULT_CONF
static ClassificationResultFormatter.FORMAT	DEFAULT_FORMAT
static java.lang.String	DEFAULT_GENE
static java.lang.String	FORMAT_DESC
static java.lang.String	FORMAT_LONG_OPT
static java.lang.String	FORMAT_SHORT_OPT
static java.lang.String	GENE_DESC
static java.lang.String	GENE_LONG_OPT
static java.lang.String	GENE_SHORT_OPT
static java.lang.String	HIER_OUTFILE_DESC
static java.lang.String	HIER_OUTFILE_LONG_OPT
static java.lang.String	HIER_OUTFILE_SHORT_OPT
static java.lang.String	METADATA_DESC
static java.lang.String	METADATA_LONG_OPT
static java.lang.String	METADATA_SHORT_OPT
static java.lang.String	MIN_BOOTSTRAP_WORDS_LONG_OPT
static java.lang.String	MIN_BOOTSTRAP_WORDS_SHORT_OPT
static java.lang.String	MIN_WORDS_DESC
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	RANK_LONG_OPT
static java.lang.String	RANK_SHORT_OPT
static java.lang.String	SAMPLE_LONG_OPT
static java.lang.String	SHORTSEQ_OUTFILE_DESC
static java.lang.String	SHORTSEQ_OUTFILE_LONG_OPT
static java.lang.String	SHORTSEQ_OUTFILE_SHORT_OPT
static java.lang.String	TAXON_LONG_OPT
static java.lang.String	TAXON_SHORT_OPT
static java.lang.String	TRAINPROPFILE_DESC
static java.lang.String	TRAINPROPFILE_LONG_OPT
static java.lang.String	TRAINPROPFILE_SHORT_OPT

Constructor Summary

Constructors

Constructor	Description
CmdOptions()

Method Summary

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_FORMAT

public static ClassificationResultFormatter.FORMAT DEFAULT_FORMAT

DEFAULT_CONF

public static float DEFAULT_CONF

DEFAULT_GENE

public static java.lang.String DEFAULT_GENE

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

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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

See Also:

Constant Field Values

GENE_LONG_OPT

public static final java.lang.String GENE_LONG_OPT

See Also:

Constant Field Values

MIN_BOOTSTRAP_WORDS_LONG_OPT

public static final java.lang.String MIN_BOOTSTRAP_WORDS_LONG_OPT

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Constant Field Values

HIER_OUTFILE_LONG_OPT

public static final java.lang.String HIER_OUTFILE_LONG_OPT

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Constant Field Values

BOOTSTRAP_LONG_OPT

public static final java.lang.String BOOTSTRAP_LONG_OPT

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Constant Field Values

RANK_LONG_OPT

public static final java.lang.String RANK_LONG_OPT

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Constant Field Values

TAXON_LONG_OPT

public static final java.lang.String TAXON_LONG_OPT

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Constant Field Values

BOOTSTRAP_OUTFILE_LONG_OPT

public static final java.lang.String BOOTSTRAP_OUTFILE_LONG_OPT

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Constant Field Values

SHORTSEQ_OUTFILE_LONG_OPT

public static final java.lang.String SHORTSEQ_OUTFILE_LONG_OPT

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Constant Field Values

BIOMFILE_LONG_OPT

public static final java.lang.String BIOMFILE_LONG_OPT

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Constant Field Values

SAMPLE_LONG_OPT

public static final java.lang.String SAMPLE_LONG_OPT

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Constant Field Values

METADATA_LONG_OPT

public static final java.lang.String METADATA_LONG_OPT

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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

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Constant Field Values

FORMAT_SHORT_OPT

public static final java.lang.String FORMAT_SHORT_OPT

See Also:

Constant Field Values

GENE_SHORT_OPT

public static final java.lang.String GENE_SHORT_OPT

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Constant Field Values

MIN_BOOTSTRAP_WORDS_SHORT_OPT

public static final java.lang.String MIN_BOOTSTRAP_WORDS_SHORT_OPT

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Constant Field Values

HIER_OUTFILE_SHORT_OPT

public static final java.lang.String HIER_OUTFILE_SHORT_OPT

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Constant Field Values

BOOTSTRAP_SHORT_OPT

public static final java.lang.String BOOTSTRAP_SHORT_OPT

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Constant Field Values

RANK_SHORT_OPT

public static final java.lang.String RANK_SHORT_OPT

See Also:

Constant Field Values

TAXON_SHORT_OPT

public static final java.lang.String TAXON_SHORT_OPT

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Constant Field Values

BOOTSTRAP_OUTFILE_SHORT_OPT

public static final java.lang.String BOOTSTRAP_OUTFILE_SHORT_OPT

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Constant Field Values

SHORTSEQ_OUTFILE_SHORT_OPT

public static final java.lang.String SHORTSEQ_OUTFILE_SHORT_OPT

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Constant Field Values

BIOMFILE_SHORT_OPT

public static final java.lang.String BIOMFILE_SHORT_OPT

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Constant Field Values

METADATA_SHORT_OPT

public static final java.lang.String METADATA_SHORT_OPT

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Constant Field Values

QUERYFILE_DESC

public static final java.lang.String QUERYFILE_DESC

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Constant Field Values

OUTFILE_DESC

public static final java.lang.String OUTFILE_DESC

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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

GENE_DESC

public static final java.lang.String GENE_DESC

MIN_WORDS_DESC

public static final java.lang.String MIN_WORDS_DESC

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Constant Field Values

HIER_OUTFILE_DESC

public static final java.lang.String HIER_OUTFILE_DESC

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Constant Field Values

BOOTSTRAP_DESC

public static final java.lang.String BOOTSTRAP_DESC

BOOTSTRAP_OUTFILE_DESC

public static final java.lang.String BOOTSTRAP_OUTFILE_DESC

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Constant Field Values

SHORTSEQ_OUTFILE_DESC

public static final java.lang.String SHORTSEQ_OUTFILE_DESC

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Constant Field Values

BIOMFILE_DESC

public static final java.lang.String BIOMFILE_DESC

See Also:

Constant Field Values

METADATA_DESC

public static final java.lang.String METADATA_DESC

See Also:

Constant Field Values

Constructor Detail

CmdOptions

public CmdOptions()