com.compomics.util.experiment.identification.identification_parameters

Class XtandemParameters

java.lang.Object

com.compomics.util.experiment.identification.identification_parameters.XtandemParameters

All Implemented Interfaces:

IdentificationAlgorithmParameter, java.io.Serializable

public class XtandemParameters
extends java.lang.Object
implements IdentificationAlgorithmParameter

The X!Tandem specific parameters.

Author:

Marc Vaudel

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
XtandemParameters() Constructor.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	equals(IdentificationAlgorithmParameter identificationAlgorithmParameter) Indicates whether another identificationAlgorithmParameter has the same parameters.
Advocate	getAlgorithm() Returns the identification algorithm.
java.lang.Double	getDynamicRange() Returns the dynamic range for spectrum filtering.
java.lang.Double	getMaxEValue() Returns the maximal e-value searched for.
java.lang.Double	getMaximumExpectationValueRefinement() Returns the maximum expectation value to use for refinement.
java.lang.Double	getMinFragmentMz() Returns the minimal fragment m/z.
java.lang.Integer	getMinPeaksPerSpectrum() Returns the minimal number of peaks per spectrum.
java.lang.Double	getMinPrecursorMass() Returns the minimal precursor mass.
java.lang.Integer	getnPeaks() Returns the number of most intense peaks to consider.
java.lang.String	getSkylinePath() Returns the skyline path.
java.lang.Boolean	isOutputHistograms() Indicates whether histograms should be written in the result file.
java.lang.Boolean	isOutputProteins() Indicates whether the protein bloc should be included in the export.
java.lang.Boolean	isOutputSequences() Returns whether the protein sequences should be included in the protein block of the export.
java.lang.Boolean	isOutputSpectra() Indicate whether the spectra should be exported in the result file.
java.lang.Boolean	isPotentialModificationsForFullRefinment() Indicates whether the refinement modifications should be used for the full refinement.
java.lang.Boolean	isProteinQuickAcetyl() Indicates whether the protein quick acetylation option should be triggered.
java.lang.Boolean	isQuickPyrolidone() Returns whether the quick pyrolidone option should be triggered.
java.lang.Boolean	isRefine() Returns whether the second pass search should be triggered.
java.lang.Boolean	isRefinePointMutations() Indicates whether point mutations should be looked for during the refinement process.
java.lang.Boolean	isRefineSemi() Indicates whether the semi enzymatic option of the second pass search should be triggered.
java.lang.Boolean	isRefineSnaps() Sets whether snAPs should be used during the refinement process.
java.lang.Boolean	isRefineSpectrumSynthesis() Indicates whether the spectrum synthesis option should be used during the refinement process.
java.lang.Boolean	isRefineUnanticipatedCleavages() Returns whether the unanticipated cleavages option should be used during the refinement process.
java.lang.Boolean	isStpBias() Returns whether the stP bias should be triggered.
java.lang.Boolean	isUseNoiseSuppression() Indicates whether noise suppression should be used when importing spectra.
void	setDynamicRange(java.lang.Double dynamicRange) Sets the dynamic range for spectrum filtering.
void	setMaxEValue(java.lang.Double maxEValue) Sets the maximal e-value searched for.
void	setMaximumExpectationValueRefinement(java.lang.Double maximumExpectationValue) Sets the maximum expectation value to use for refinement.
void	setMinFragmentMz(java.lang.Double minFragmentMz) Sets the minimal fragment m/z.
void	setMinPeaksPerSpectrum(java.lang.Integer minPeaksPerSpectrum) Sets the minimal number of peaks per spectrum.
void	setMinPrecursorMass(java.lang.Double minPrecursorMass) Sets the minimal precursor mass.
void	setnPeaks(java.lang.Integer nPeaks) Sets the number of most intense peaks to consider.
void	setOutputHistograms(java.lang.Boolean outputHistograms) Sets whether histograms should be written in the result file
void	setOutputProteins(java.lang.Boolean outputProteins) Sets whether the protein bloc should be included in the export.
void	setOutputSequences(boolean outputSequences) Sets whether the protein sequences should be included in the protein block of the export.
void	setOutputSpectra(java.lang.Boolean outputSpectra) Sets whether the spectra should be exported in the result file.
void	setPotentialModificationsForFullRefinment(java.lang.Boolean potentialModificationsForFullRefinment) Sets whether the refinement modifications should be used for the full refinement
void	setProteinQuickAcetyl(java.lang.Boolean proteinQuickAcetyl) Sets whether the protein quick acetylation option should be triggered.
void	setQuickPyrolidone(java.lang.Boolean quickPyrolidone) Sets whether the quick pyrolidone option should be triggered.
void	setRefine(java.lang.Boolean refine) Sets whether the second pass search should be triggered.
void	setRefinePointMutations(java.lang.Boolean refinePointMutations) Sets whether point mutations should be looked for during the refinement process.
void	setRefineSemi(java.lang.Boolean refineSemi) Sets whether the semi enzymatic option of the second pass search should be triggered.
void	setRefineSnaps(java.lang.Boolean refineSnaps) Sets whether snAPs should be used during the refinement process.
void	setRefineSpectrumSynthesis(java.lang.Boolean refineSpectrumSynthesis) Sets whether the spectrum synthesis option should be used during the refinement process.
void	setRefineUnanticipatedCleavages(java.lang.Boolean refineUnanticipatedCleavages) Sets whether the unanticipated cleavages option should be used during the refinement process.
void	setSkylinePath(java.lang.String skylinePath) Sets the skyline path.
void	setStpBias(java.lang.Boolean stpBias) Sets whether the stP bias should be triggered
void	setUseNoiseSuppression(java.lang.Boolean useNoiseSuppression) Sets whether noise suppression should be used when importing spectra.
java.lang.String	toString(boolean html) Returns the parameters as a string.

Methods inherited from class java.lang.Object

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

Constructor Detail

XtandemParameters

public XtandemParameters()

Constructor.

Method Detail

getDynamicRange

public java.lang.Double getDynamicRange()

Returns the dynamic range for spectrum filtering.

Returns:

the dynamic range for spectrum filtering

setDynamicRange

public void setDynamicRange(java.lang.Double dynamicRange)

Sets the dynamic range for spectrum filtering.

Parameters:

dynamicRange - the dynamic range for spectrum filtering

getnPeaks

public java.lang.Integer getnPeaks()

Returns the number of most intense peaks to consider.

Returns:

the number of most intense peaks to consider

setnPeaks

public void setnPeaks(java.lang.Integer nPeaks)

Sets the number of most intense peaks to consider.

Parameters:

nPeaks - the number of most intense peaks to consider

getMinPrecursorMass

public java.lang.Double getMinPrecursorMass()

Returns the minimal precursor mass.

Returns:

the minimal precursor mass

setMinPrecursorMass

public void setMinPrecursorMass(java.lang.Double minPrecursorMass)

Sets the minimal precursor mass.

Parameters:

minPrecursorMass - the minimal precursor mass

getMinFragmentMz

public java.lang.Double getMinFragmentMz()

Returns the minimal fragment m/z.

Returns:

the minimal fragment m/z

setMinFragmentMz

public void setMinFragmentMz(java.lang.Double minFragmentMz)

Sets the minimal fragment m/z.

Parameters:

minFragmentMz - the minimal fragment m/z

getMinPeaksPerSpectrum

public java.lang.Integer getMinPeaksPerSpectrum()

Returns the minimal number of peaks per spectrum.

Returns:

the minimal number of peaks per spectrum

setMinPeaksPerSpectrum

public void setMinPeaksPerSpectrum(java.lang.Integer minPeaksPerSpectrum)

Sets the minimal number of peaks per spectrum.

Parameters:

minPeaksPerSpectrum - the minimal number of peaks per spectrum

isProteinQuickAcetyl

public java.lang.Boolean isProteinQuickAcetyl()

Indicates whether the protein quick acetylation option should be triggered.

Returns:

true if the protein quick acetylation option should be triggered

setProteinQuickAcetyl

public void setProteinQuickAcetyl(java.lang.Boolean proteinQuickAcetyl)

Sets whether the protein quick acetylation option should be triggered.

Parameters:

proteinQuickAcetyl - true if the protein quick acetylation option should be triggered

isQuickPyrolidone

public java.lang.Boolean isQuickPyrolidone()

Returns whether the quick pyrolidone option should be triggered.

Returns:

true if the quick pyrolidone option should be triggered

setQuickPyrolidone

public void setQuickPyrolidone(java.lang.Boolean quickPyrolidone)

Sets whether the quick pyrolidone option should be triggered.

Parameters:

quickPyrolidone - the quick pyrolidone option should be triggered

isRefine

public java.lang.Boolean isRefine()

Returns whether the second pass search should be triggered.

Returns:

true if the second pass search should be triggered

setRefine

public void setRefine(java.lang.Boolean refine)

Sets whether the second pass search should be triggered.

Parameters:

refine - true if the second pass search should be triggered

isStpBias

public java.lang.Boolean isStpBias()

Returns whether the stP bias should be triggered.

Returns:

true if the stP bias should be triggered

setStpBias

public void setStpBias(java.lang.Boolean stpBias)

Sets whether the stP bias should be triggered

Parameters:

stpBias - true if the stP bias should be triggered

getMaxEValue

public java.lang.Double getMaxEValue()

Returns the maximal e-value searched for.

Returns:

the maximal e-value searched for

setMaxEValue

public void setMaxEValue(java.lang.Double maxEValue)

Sets the maximal e-value searched for.

Parameters:

maxEValue - the maximal e-value searched for

isRefineSemi

public java.lang.Boolean isRefineSemi()

Indicates whether the semi enzymatic option of the second pass search should be triggered.

Returns:

true if the semi enzymatic option of the second pass search should be triggered

setRefineSemi

public void setRefineSemi(java.lang.Boolean refineSemi)

Sets whether the semi enzymatic option of the second pass search should be triggered.

Parameters:

refineSemi - true if the semi enzymatic option of the second pass search should be triggered

isRefinePointMutations

public java.lang.Boolean isRefinePointMutations()

Indicates whether point mutations should be looked for during the refinement process.

Returns:

true if point mutations should be looked for during the refinement process

setRefinePointMutations

public void setRefinePointMutations(java.lang.Boolean refinePointMutations)

Sets whether point mutations should be looked for during the refinement process.

Parameters:

refinePointMutations - true if point mutations should be looked for during the refinement process

isRefineSpectrumSynthesis

public java.lang.Boolean isRefineSpectrumSynthesis()

Indicates whether the spectrum synthesis option should be used during the refinement process.

Returns:

true if the spectrum synthesis option should be used during the refinement process

setRefineSpectrumSynthesis

public void setRefineSpectrumSynthesis(java.lang.Boolean refineSpectrumSynthesis)

Sets whether the spectrum synthesis option should be used during the refinement process.

Parameters:

refineSpectrumSynthesis - true if the spectrum synthesis option should be used during the refinement process

isRefineUnanticipatedCleavages

public java.lang.Boolean isRefineUnanticipatedCleavages()

Returns whether the unanticipated cleavages option should be used during the refinement process.

Returns:

true if the unanticipated cleavages option should be used during the refinement process

setRefineUnanticipatedCleavages

public void setRefineUnanticipatedCleavages(java.lang.Boolean refineUnanticipatedCleavages)

Sets whether the unanticipated cleavages option should be used during the refinement process.

Parameters:

refineUnanticipatedCleavages - true if the unanticipated cleavages option should be used during the refinement process

getMaximumExpectationValueRefinement

public java.lang.Double getMaximumExpectationValueRefinement()

Returns the maximum expectation value to use for refinement.

Returns:

the maximum expectation value to use for refinement

setMaximumExpectationValueRefinement

public void setMaximumExpectationValueRefinement(java.lang.Double maximumExpectationValue)

Sets the maximum expectation value to use for refinement.

Parameters:

maximumExpectationValue - the maximum expectation value to use for refinement

isPotentialModificationsForFullRefinment

public java.lang.Boolean isPotentialModificationsForFullRefinment()

Indicates whether the refinement modifications should be used for the full refinement.

Returns:

true if the refinement modifications should be used for the full refinement

setPotentialModificationsForFullRefinment

public void setPotentialModificationsForFullRefinment(java.lang.Boolean potentialModificationsForFullRefinment)

Sets whether the refinement modifications should be used for the full refinement

Parameters:

potentialModificationsForFullRefinment - true if the refinement modifications should be used for the full refinement

getSkylinePath

public java.lang.String getSkylinePath()

Returns the skyline path.

Returns:

the skyline path

setSkylinePath

public void setSkylinePath(java.lang.String skylinePath)

Sets the skyline path.

Parameters:

skylinePath - the skyline path

isOutputProteins

public java.lang.Boolean isOutputProteins()

Indicates whether the protein bloc should be included in the export.

Returns:

true if the protein bloc should be included in the export

setOutputProteins

public void setOutputProteins(java.lang.Boolean outputProteins)

Sets whether the protein bloc should be included in the export.

Parameters:

outputProteins - the protein bloc should be included in the export

isOutputSequences

public java.lang.Boolean isOutputSequences()

Returns whether the protein sequences should be included in the protein block of the export.

Returns:

true if the protein sequences should be included in the protein block of the export

setOutputSequences

public void setOutputSequences(boolean outputSequences)

Sets whether the protein sequences should be included in the protein block of the export.

Parameters:

outputSequences - true if the protein sequences should be included in the protein block of the export

isOutputSpectra

public java.lang.Boolean isOutputSpectra()

Indicate whether the spectra should be exported in the result file.

Returns:

true if the spectra should be exported in the result file

setOutputSpectra

public void setOutputSpectra(java.lang.Boolean outputSpectra)

Sets whether the spectra should be exported in the result file.

Parameters:

outputSpectra - true if the spectra should be exported in the result file

isOutputHistograms

public java.lang.Boolean isOutputHistograms()

Indicates whether histograms should be written in the result file.

Returns:

true if histograms should be written in the result file

setOutputHistograms

public void setOutputHistograms(java.lang.Boolean outputHistograms)

Sets whether histograms should be written in the result file

Parameters:

outputHistograms - true if histograms should be written in the result file

isUseNoiseSuppression

public java.lang.Boolean isUseNoiseSuppression()

Indicates whether noise suppression should be used when importing spectra.

Returns:

true if noise suppression should be used when importing spectra

setUseNoiseSuppression

public void setUseNoiseSuppression(java.lang.Boolean useNoiseSuppression)

Sets whether noise suppression should be used when importing spectra.

Parameters:

useNoiseSuppression - true if noise suppression should be used when importing spectra

isRefineSnaps

public java.lang.Boolean isRefineSnaps()

Sets whether snAPs should be used during the refinement process.

Returns:

true if snAPs should be used during the refinement process

setRefineSnaps

public void setRefineSnaps(java.lang.Boolean refineSnaps)

Sets whether snAPs should be used during the refinement process.

Parameters:

refineSnaps - true if snAPs should be used during the refinement process

getAlgorithm

public Advocate getAlgorithm()

Description copied from interface: IdentificationAlgorithmParameter

Returns the identification algorithm.

Specified by:

getAlgorithm in interface IdentificationAlgorithmParameter

Returns:

the identification algorithm

equals

public boolean equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)

Description copied from interface: IdentificationAlgorithmParameter

Indicates whether another identificationAlgorithmParameter has the same parameters.

Specified by:

equals in interface IdentificationAlgorithmParameter

Parameters:

identificationAlgorithmParameter - the other identificationAlgorithmParameter

Returns:

true if the algorithm and parameters are the same

toString

public java.lang.String toString(boolean html)

Description copied from interface: IdentificationAlgorithmParameter

Returns the parameters as a string.

Specified by:

toString in interface IdentificationAlgorithmParameter

Parameters:

html - use HTML formatting

Returns:

the parameters as a string