Class XtandemParameters
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.tool_specific.XtandemParameters
- All Implemented Interfaces:
IdentificationAlgorithmParameter
,Serializable
public class XtandemParameters extends ExperimentObject implements IdentificationAlgorithmParameter
The X!Tandem specific parameters.
- Author:
- Marc Vaudel
- See Also:
- Serialized Form
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Field Summary
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Constructor Summary
Constructors Constructor Description XtandemParameters()
Constructor. -
Method Summary
Modifier and Type Method Description boolean
equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
Indicates whether another identificationAlgorithmParameter has the same parameters.Advocate
getAlgorithm()
Returns the identification algorithm.double
getDynamicRange()
Returns the dynamic range for spectrum filtering.double
getMaxEValue()
Returns the maximal e-value searched for.double
getMaximumExpectationValueRefinement()
Returns the maximum expectation value to use for refinement.double
getMinFragmentMz()
Returns the minimal fragment m/z.int
getMinPeaksPerSpectrum()
Returns the minimal number of peaks per spectrum.double
getMinPrecursorMass()
Returns the minimal precursor mass.int
getnPeaks()
Returns the number of most intense peaks to consider.String
getOutputResults()
Returns the output results filter.boolean
getParentMonoisotopicMassIsotopeError()
Returns true if the parent ion mass tolerance is expanded by opening up multiple tolerance windows centered on the first and second 13C isotope peaks for a peptide.double
getProteinPtmComplexity()
Returns the proteinPtmComplexity.String
getSkylinePath()
Returns the skyline path.boolean
isOutputHistograms()
Indicates whether histograms should be written in the result file.boolean
isOutputProteins()
Indicates whether the protein bloc should be included in the export.boolean
isOutputSequences()
Returns whether the protein sequences should be included in the protein block of the export.boolean
isOutputSpectra()
Indicate whether the spectra should be exported in the result file.boolean
isPotentialModificationsForFullRefinment()
Indicates whether the refinement modifications should be used for the full refinement.boolean
isProteinQuickAcetyl()
Indicates whether the protein quick acetylation option should be triggered.boolean
isQuickPyrolidone()
Returns whether the quick pyrolidone option should be triggered.boolean
isRefine()
Returns whether the second pass search should be triggered.boolean
isRefinePointMutations()
Indicates whether point mutations should be looked for during the refinement process.boolean
isRefineSemi()
Indicates whether the semi enzymatic option of the second pass search should be triggered.boolean
isRefineSnaps()
Sets whether snAPs should be used during the refinement process.boolean
isRefineSpectrumSynthesis()
Indicates whether the spectrum synthesis option should be used during the refinement process.boolean
isRefineUnanticipatedCleavages()
Returns whether the unanticipated cleavages option should be used during the refinement process.boolean
isStpBias()
Returns whether the stP bias should be triggered.boolean
isUseNoiseSuppression()
Indicates whether noise suppression should be used when importing spectra.void
setDynamicRange(double dynamicRange)
Sets the dynamic range for spectrum filtering.void
setMaxEValue(double maxEValue)
Sets the maximal e-value searched for.void
setMaximumExpectationValueRefinement(double maximumExpectationValue)
Sets the maximum expectation value to use for refinement.void
setMinFragmentMz(double minFragmentMz)
Sets the minimal fragment m/z.void
setMinPeaksPerSpectrum(int minPeaksPerSpectrum)
Sets the minimal number of peaks per spectrum.void
setMinPrecursorMass(double minPrecursorMass)
Sets the minimal precursor mass.void
setnPeaks(int nPeaks)
Sets the number of most intense peaks to consider.void
setOutputHistograms(boolean outputHistograms)
Sets whether histograms should be written in the result filevoid
setOutputProteins(boolean outputProteins)
Sets whether the protein bloc should be included in the export.void
setOutputResults(String outputResults)
Set the output results filter.void
setOutputSequences(boolean outputSequences)
Sets whether the protein sequences should be included in the protein block of the export.void
setOutputSpectra(boolean outputSpectra)
Sets whether the spectra should be exported in the result file.void
setParentMonoisotopicMassIsotopeError(boolean parentMonoisotopicMassIsotopeError)
Sets whether the parent ion mass tolerance is expanded by opening up multiple tolerance windows centered on the first and second 13C isotope peaks for a peptide.void
setPotentialModificationsForFullRefinment(boolean potentialModificationsForFullRefinment)
Sets whether the refinement modifications should be used for the full refinementvoid
setProteinPtmComplexity(double proteinPtmComplexity)
Set the proteinPtmComplexity.void
setProteinQuickAcetyl(boolean proteinQuickAcetyl)
Sets whether the protein quick acetylation option should be triggered.void
setQuickPyrolidone(boolean quickPyrolidone)
Sets whether the quick pyrolidone option should be triggered.void
setRefine(boolean refine)
Sets whether the second pass search should be triggered.void
setRefinePointMutations(boolean refinePointMutations)
Sets whether point mutations should be looked for during the refinement process.void
setRefineSemi(boolean refineSemi)
Sets whether the semi enzymatic option of the second pass search should be triggered.void
setRefineSnaps(boolean refineSnaps)
Sets whether snAPs should be used during the refinement process.void
setRefineSpectrumSynthesis(boolean refineSpectrumSynthesis)
Sets whether the spectrum synthesis option should be used during the refinement process.void
setRefineUnanticipatedCleavages(boolean refineUnanticipatedCleavages)
Sets whether the unanticipated cleavages option should be used during the refinement process.void
setSkylinePath(String skylinePath)
Sets the skyline path.void
setStpBias(boolean stpBias)
Sets whether the stP bias should be triggeredvoid
setUseNoiseSuppression(boolean useNoiseSuppression)
Sets whether noise suppression should be used when importing spectra.String
toString(boolean html)
Returns the parameters as a string.Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
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Constructor Details
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XtandemParameters
public XtandemParameters()Constructor.
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Method Details
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getDynamicRange
public double getDynamicRange()Returns the dynamic range for spectrum filtering.- Returns:
- the dynamic range for spectrum filtering
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setDynamicRange
public void setDynamicRange(double dynamicRange)Sets the dynamic range for spectrum filtering.- Parameters:
dynamicRange
- the dynamic range for spectrum filtering
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getnPeaks
public int getnPeaks()Returns the number of most intense peaks to consider.- Returns:
- the number of most intense peaks to consider
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setnPeaks
public void setnPeaks(int nPeaks)Sets the number of most intense peaks to consider.- Parameters:
nPeaks
- the number of most intense peaks to consider
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getMinPrecursorMass
public double getMinPrecursorMass()Returns the minimal precursor mass.- Returns:
- the minimal precursor mass
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setMinPrecursorMass
public void setMinPrecursorMass(double minPrecursorMass)Sets the minimal precursor mass.- Parameters:
minPrecursorMass
- the minimal precursor mass
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getMinFragmentMz
public double getMinFragmentMz()Returns the minimal fragment m/z.- Returns:
- the minimal fragment m/z
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setMinFragmentMz
public void setMinFragmentMz(double minFragmentMz)Sets the minimal fragment m/z.- Parameters:
minFragmentMz
- the minimal fragment m/z
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getMinPeaksPerSpectrum
public int getMinPeaksPerSpectrum()Returns the minimal number of peaks per spectrum.- Returns:
- the minimal number of peaks per spectrum
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setMinPeaksPerSpectrum
public void setMinPeaksPerSpectrum(int minPeaksPerSpectrum)Sets the minimal number of peaks per spectrum.- Parameters:
minPeaksPerSpectrum
- the minimal number of peaks per spectrum
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isProteinQuickAcetyl
public boolean isProteinQuickAcetyl()Indicates whether the protein quick acetylation option should be triggered.- Returns:
- true if the protein quick acetylation option should be triggered
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setProteinQuickAcetyl
public void setProteinQuickAcetyl(boolean proteinQuickAcetyl)Sets whether the protein quick acetylation option should be triggered.- Parameters:
proteinQuickAcetyl
- true if the protein quick acetylation option should be triggered
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isQuickPyrolidone
public boolean isQuickPyrolidone()Returns whether the quick pyrolidone option should be triggered.- Returns:
- true if the quick pyrolidone option should be triggered
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setQuickPyrolidone
public void setQuickPyrolidone(boolean quickPyrolidone)Sets whether the quick pyrolidone option should be triggered.- Parameters:
quickPyrolidone
- the quick pyrolidone option should be triggered
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isRefine
public boolean isRefine()Returns whether the second pass search should be triggered.- Returns:
- true if the second pass search should be triggered
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setRefine
public void setRefine(boolean refine)Sets whether the second pass search should be triggered.- Parameters:
refine
- true if the second pass search should be triggered
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isStpBias
public boolean isStpBias()Returns whether the stP bias should be triggered.- Returns:
- true if the stP bias should be triggered
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setStpBias
public void setStpBias(boolean stpBias)Sets whether the stP bias should be triggered- Parameters:
stpBias
- true if the stP bias should be triggered
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getMaxEValue
public double getMaxEValue()Returns the maximal e-value searched for.- Returns:
- the maximal e-value searched for
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setMaxEValue
public void setMaxEValue(double maxEValue)Sets the maximal e-value searched for.- Parameters:
maxEValue
- the maximal e-value searched for
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isRefineSemi
public 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
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setRefineSemi
public void setRefineSemi(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
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isRefinePointMutations
public 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
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setRefinePointMutations
public void setRefinePointMutations(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
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isRefineSpectrumSynthesis
public 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
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setRefineSpectrumSynthesis
public void setRefineSpectrumSynthesis(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
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isRefineUnanticipatedCleavages
public 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
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setRefineUnanticipatedCleavages
public void setRefineUnanticipatedCleavages(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
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getMaximumExpectationValueRefinement
public double getMaximumExpectationValueRefinement()Returns the maximum expectation value to use for refinement.- Returns:
- the maximum expectation value to use for refinement
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setMaximumExpectationValueRefinement
public void setMaximumExpectationValueRefinement(double maximumExpectationValue)Sets the maximum expectation value to use for refinement.- Parameters:
maximumExpectationValue
- the maximum expectation value to use for refinement
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isPotentialModificationsForFullRefinment
public 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
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setPotentialModificationsForFullRefinment
public void setPotentialModificationsForFullRefinment(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
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getSkylinePath
Returns the skyline path.- Returns:
- the skyline path
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setSkylinePath
Sets the skyline path.- Parameters:
skylinePath
- the skyline path
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isOutputProteins
public 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
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setOutputProteins
public void setOutputProteins(boolean outputProteins)Sets whether the protein bloc should be included in the export.- Parameters:
outputProteins
- the protein bloc should be included in the export
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isOutputSequences
public 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
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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
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isOutputSpectra
public 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
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setOutputSpectra
public void setOutputSpectra(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
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isOutputHistograms
public boolean isOutputHistograms()Indicates whether histograms should be written in the result file.- Returns:
- true if histograms should be written in the result file
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setOutputHistograms
public void setOutputHistograms(boolean outputHistograms)Sets whether histograms should be written in the result file- Parameters:
outputHistograms
- true if histograms should be written in the result file
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isUseNoiseSuppression
public boolean isUseNoiseSuppression()Indicates whether noise suppression should be used when importing spectra. Note: ignored in X!Tandem VENGEANCE (2015.12.15) and newer- Returns:
- true if noise suppression should be used when importing spectra
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setUseNoiseSuppression
public void setUseNoiseSuppression(boolean useNoiseSuppression)Sets whether noise suppression should be used when importing spectra. Note: ignored in X!Tandem VENGEANCE (2015.12.15) and newer- Parameters:
useNoiseSuppression
- true if noise suppression should be used when importing spectra
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isRefineSnaps
public boolean isRefineSnaps()Sets whether snAPs should be used during the refinement process.- Returns:
- true if snAPs should be used during the refinement process
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setRefineSnaps
public void setRefineSnaps(boolean refineSnaps)Sets whether snAPs should be used during the refinement process.- Parameters:
refineSnaps
- true if snAPs should be used during the refinement process
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getOutputResults
Returns the output results filter.- Returns:
- the outputResults
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setOutputResults
Set the output results filter.- Parameters:
outputResults
- the outputResults to set
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getProteinPtmComplexity
public double getProteinPtmComplexity()Returns the proteinPtmComplexity.- Returns:
- the proteinPtmComplexity
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setProteinPtmComplexity
public void setProteinPtmComplexity(double proteinPtmComplexity)Set the proteinPtmComplexity.- Parameters:
proteinPtmComplexity
- the proteinPtmComplexity to set
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getAlgorithm
Description copied from interface:IdentificationAlgorithmParameter
Returns the identification algorithm.- Specified by:
getAlgorithm
in interfaceIdentificationAlgorithmParameter
- Returns:
- the identification algorithm
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equals
Description copied from interface:IdentificationAlgorithmParameter
Indicates whether another identificationAlgorithmParameter has the same parameters.- Specified by:
equals
in interfaceIdentificationAlgorithmParameter
- Parameters:
identificationAlgorithmParameter
- the other identificationAlgorithmParameter- Returns:
- true if the algorithm and parameters are the same
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toString
Description copied from interface:IdentificationAlgorithmParameter
Returns the parameters as a string.- Specified by:
toString
in interfaceIdentificationAlgorithmParameter
- Parameters:
html
- use HTML formatting- Returns:
- the parameters as a string
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getParentMonoisotopicMassIsotopeError
public boolean getParentMonoisotopicMassIsotopeError()Returns true if the parent ion mass tolerance is expanded by opening up multiple tolerance windows centered on the first and second 13C isotope peaks for a peptide.- Returns:
- the parentMonoisotopicMassIsotopeError
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setParentMonoisotopicMassIsotopeError
public void setParentMonoisotopicMassIsotopeError(boolean parentMonoisotopicMassIsotopeError)Sets whether the parent ion mass tolerance is expanded by opening up multiple tolerance windows centered on the first and second 13C isotope peaks for a peptide.- Parameters:
parentMonoisotopicMassIsotopeError
- the parentMonoisotopicMassIsotopeError to set
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