Class TideParameters
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.tool_specific.TideParameters
- All Implemented Interfaces:
IdentificationAlgorithmParameter
,Serializable
public class TideParameters extends ExperimentObject implements IdentificationAlgorithmParameter
The Tide specific parameters.
- Author:
- Harald Barsnes
- See Also:
- Serialized Form
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Field Summary
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Constructor Summary
Constructors Constructor Description TideParameters()
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.Boolean
getClipNtermMethionine()
Returns if the starting methionine peptides will be included both with and without the starting M.Boolean
getComputeExactPValues()
Returns true if the exact p-values are to be computed.Boolean
getComputeSpScore()
Returns true of the SP score is to be computed.Boolean
getConcatenatTargetDecoy()
Returns true if the target and decoy results are to be concatenated.String
getDecoyFormat()
Returns the decoy format.Integer
getDecoySeed()
Returns the decoy seed.String
getDigestionType()
Returns the enzyme digestion type.String
getFastIndexFolderName()
Returns the name of the FASTA index folder.String
getKeepTerminalAminoAcids()
Returns the option for keeping the terminal amino acids when generating the decoys.Integer
getMaxPeptideLength()
Returns the maximal peptide length allowed.Double
getMaxPrecursorMass()
Returns the maxPrecursorMass precursor mass.Double
getMaxSpectrumMz()
Returns the max spectrum m/z to search for.Integer
getMaxVariableModificationsPerPeptide()
Returns the maximum number of variable modifications allowed on a single peptide.Integer
getMaxVariableModificationsPerTypePerPeptide()
Returns the maximum number of variable modifications of each modification type allowed on a single peptide.Integer
getMinPeptideLength()
Sets the minimal peptide length allowed.Double
getMinPrecursorMass()
Returns the minimum precursor mass.Double
getMinSpectrumMz()
Return the min spectrum m/z to search for.Integer
getMinSpectrumPeaks()
Returns the min number of peaks in a spectrum.Boolean
getMonoisotopicPrecursor()
Returns true if the precursor mass is monoisotopic, false if average.Double
getMzBinOffset()
Returns the m/z bin offset.Double
getMzBinWidth()
Returns the m/z bin width.Boolean
getMzidOutput()
Returns true if the mzid output is to be created.Integer
getNumberOfSpectrumMatches()
Returns the number of PSMs to report per spectrum.String
getOutputFolderName()
Returns the name of the output folder.Boolean
getPepXmlOutput()
Returns true if the pepxml output is to be created.Boolean
getPinOutput()
Returns true if the Percolator output is to be created.Boolean
getPrintPeptides()
Returns true of a list of the peptides should be printed to the output folder.Integer
getPrintProgressIndicatorSize()
Returns the progress indicator size.Boolean
getRemovePrecursor()
Returns true of the precursor peak is to be removed.Double
getRemovePrecursorTolerance()
Returns the tolerance with which to remove the precursor peak.Boolean
getRemoveTempFolders()
Returns true if the output and index folders are to be removed when the search has completed.String
getSpectrumCharges()
Returns the spectrum charges to search for.Boolean
getSqtOutput()
Returns true if the sqt output is to be created.String
getStoreSpectraFileName()
Returns the name of the file where the binary spectra are to be stored.Boolean
getTextOutput()
Returns true if the text output is to be created.Boolean
getUseFlankingPeaks()
Returns true if flanking peaks are to be used.Boolean
getUseNeutralLossPeaks()
Returns true if the neutral loss peaks are to be used.Integer
getVerbosity()
Returns the verbosity type of progress output.void
setClipNtermMethionine(Boolean clipNtermMethionine)
Set if the starting methionine peptides will be included both with and without the starting M.void
setComputeExactPValues(Boolean computeExactPValues)
Set if the exact p-values are to be computed.void
setComputeSpScore(Boolean computeSpScore)
Set if the SP score is to be computed.void
setConcatenatTargetDecoy(Boolean concatenate)
Set if the target and decoy results are to be concatenated.void
setDecoyFormat(String decoyFormat)
Set the decoy format.void
setDecoySeed(Integer decoySeed)
Set the decoy seed.void
setDigestionType(String digestionType)
Set the enzyme digestion type.void
setFastIndexFolderName(String fastIndexFolderName)
Set the name of the FASTA index folder.void
setKeepTerminalAminoAcids(String keepTerminalAminoAcids)
Set the option for keeping the terminal amino acids when generating the decoysvoid
setMaxPeptideLength(Integer maxPeptideLength)
Sets the maximal peptide length allowed.void
setMaxPrecursorMass(Double maxPrecursorMass)
Sets the maximum precursor mass.void
setMaxSpectrumMz(Double maxSpectrumMz)
Set the max spectrum m/z to search for.void
setMaxVariableModificationsPerPeptide(Integer maxVariableModificationsPerPeptide)
Set the maximum number of variable modifications of allowed on a single peptide.void
setMaxVariableModificationsPerTypePerPeptide(Integer maxVariableModificationsPerTypePerPeptide)
Set the maximum number of variable modifications of each modification type allowed on a single peptide.void
setMinPeptideLength(Integer minPeptideLength)
Sets the minimal peptide length allowed.void
setMinPrecursorMass(Double minPrecursorMass)
Sets the minimum precursor mass.void
setMinSpectrumMz(Double minSpectrumMz)
Set the min spectrum m/z to search for.void
setMinSpectrumPeaks(Integer minSpectrumPeaks)
Set the min number of peaks in a spectrum.void
setMonoisotopicPrecursor(Boolean monoisotopicPrecursor)
Set if the precursor mass is monoisotopic.void
setMzBinOffset(Double mzBinOffset)
Set the m/z bin offset.void
setMzBinWidth(Double mzBinWidth)
Set the m/z bin width.void
setMzidOutput(Boolean mzidOutput)
Set if the mzid output is to be created.void
setNumberOfSpectrumMatches(Integer numberOfSpectrumMatches)
Set the number of PSMs to report per spectrum.void
setOutputFolderName(String outputFolderName)
Set the name of the output folder.void
setPepXmlOutput(Boolean pepXmlOutput)
Set if the pepxml output is to be created.void
setPinOutput(Boolean pinOutput)
Set if the Percolator output is to be created.void
setPrintPeptides(Boolean printPeptides)
Set if a list of the peptides should be printed to the output folder.void
setPrintProgressIndicatorSize(Integer printProgressIndicatorSize)
Set the progress indicator size.void
setRemovePrecursor(Boolean removePrecursor)
Set if the precursor peak is to be removed.void
setRemovePrecursorTolerance(Double removePrecursorTolerance)
Set the tolerance with which to remove the precursor peak.void
setRemoveTempFolders(Boolean removeTempFolders)
Set if the output and index folders are to be removed when the search has completed.void
setSpectrumCharges(String spectrumCharges)
Set the spectrum charges to search for.void
setSqtOutput(Boolean sqtOutput)
Set if the sqt output is to be created.void
setStoreSpectraFileName(String storeSpectraFileName)
Set the name of the file where the binary spectra are to be stored.void
setTextOutput(Boolean textOutput)
Set if the text output is to be created.void
setUseFlankingPeaks(Boolean useFlankingPeaks)
Set if flanking peaks are to be used.void
setUseNeutralLossPeaks(Boolean useNeutralLossPeaks)
Set if the neutral loss peaks are to be used.void
setVerbosity(Integer verbosity)
Set the verbosity type of progress output.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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TideParameters
public TideParameters()Constructor.
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Method Details
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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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getMaxVariableModificationsPerPeptide
Returns the maximum number of variable modifications allowed on a single peptide. Null if no upper limit is set.- Returns:
- the maxVariableModificationsPerPeptide
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setMaxVariableModificationsPerPeptide
Set the maximum number of variable modifications of allowed on a single peptide. Set to null if no upper limit is to be used.- Parameters:
maxVariableModificationsPerPeptide
- the maxVariableModificationsPerPeptide to set
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getMaxVariableModificationsPerTypePerPeptide
Returns the maximum number of variable modifications of each modification type allowed on a single peptide. Null if no upper limit is set.- Returns:
- the maxVariableModificationsPerTypePerPeptide
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setMaxVariableModificationsPerTypePerPeptide
public void setMaxVariableModificationsPerTypePerPeptide(Integer maxVariableModificationsPerTypePerPeptide)Set the maximum number of variable modifications of each modification type allowed on a single peptide. Set to null if no upper limit is to be used.- Parameters:
maxVariableModificationsPerTypePerPeptide
- the maxVariableModificationsPerTypePerPeptide to set
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getMaxPeptideLength
Returns the maximal peptide length allowed.- Returns:
- the maximal peptide length allowed
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setMaxPeptideLength
Sets the maximal peptide length allowed.- Parameters:
maxPeptideLength
- the maximal peptide length allowed
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getMinPeptideLength
Sets the minimal peptide length allowed.- Returns:
- the minimal peptide length allowed
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setMinPeptideLength
Sets the minimal peptide length allowed.- Parameters:
minPeptideLength
- the minimal peptide length allowed
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getMinPrecursorMass
Returns the minimum precursor mass.- Returns:
- the minimum precursor mass
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setMinPrecursorMass
Sets the minimum precursor mass.- Parameters:
minPrecursorMass
- the minPrecursorMass to set
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getMaxPrecursorMass
Returns the maxPrecursorMass precursor mass.- Returns:
- the maximum precursor mass
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setMaxPrecursorMass
Sets the maximum precursor mass.- Parameters:
maxPrecursorMass
- the maximum to set
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getDecoyFormat
Returns the decoy format.- Returns:
- the decoyFormat
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setDecoyFormat
Set the decoy format.- Parameters:
decoyFormat
- the decoyFormat to set
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getKeepTerminalAminoAcids
Returns the option for keeping the terminal amino acids when generating the decoys.- Returns:
- the keepTerminalAminoAcids
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setKeepTerminalAminoAcids
Set the option for keeping the terminal amino acids when generating the decoys- Parameters:
keepTerminalAminoAcids
- the keepTerminalAminoAcids to set
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getDecoySeed
Returns the decoy seed.- Returns:
- the decoySeed
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setDecoySeed
Set the decoy seed.- Parameters:
decoySeed
- the decoySeed to set
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getOutputFolderName
Returns the name of the output folder.- Returns:
- the outputFolderName
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setOutputFolderName
Set the name of the output folder.- Parameters:
outputFolderName
- the outputFolderName to set
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getPrintPeptides
Returns true of a list of the peptides should be printed to the output folder.- Returns:
- the printPeptides
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setPrintPeptides
Set if a list of the peptides should be printed to the output folder.- Parameters:
printPeptides
- the printPeptides to set
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getVerbosity
Returns the verbosity type of progress output.- Returns:
- the verbosity
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setVerbosity
Set the verbosity type of progress output.- Parameters:
verbosity
- the verbosity to set
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getMonoisotopicPrecursor
Returns true if the precursor mass is monoisotopic, false if average.- Returns:
- the monoisotopicPrecursor
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setMonoisotopicPrecursor
Set if the precursor mass is monoisotopic.- Parameters:
monoisotopicPrecursor
- the monoisotopicPrecursor to set
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getClipNtermMethionine
Returns if the starting methionine peptides will be included both with and without the starting M.- Returns:
- the clipNtermMethionine
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setClipNtermMethionine
Set if the starting methionine peptides will be included both with and without the starting M.- Parameters:
clipNtermMethionine
- the clipNtermMethionine to set
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getDigestionType
Returns the enzyme digestion type.- Returns:
- the digestionType
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setDigestionType
Set the enzyme digestion type.- Parameters:
digestionType
- the digestionType to set
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getComputeSpScore
Returns true of the SP score is to be computed.- Returns:
- the computeSpScore
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setComputeSpScore
Set if the SP score is to be computed.- Parameters:
computeSpScore
- the computeSpScore to set
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getNumberOfSpectrumMatches
Returns the number of PSMs to report per spectrum.- Returns:
- the numberOfSpectrumMatches
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setNumberOfSpectrumMatches
Set the number of PSMs to report per spectrum.- Parameters:
numberOfSpectrumMatches
- the numberOfSpectrumMatches to set
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getComputeExactPValues
Returns true if the exact p-values are to be computed.- Returns:
- the computeExactPValues
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setComputeExactPValues
Set if the exact p-values are to be computed.- Parameters:
computeExactPValues
- the computeExactPValues to set
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getMinSpectrumMz
Return the min spectrum m/z to search for.- Returns:
- the minSpectrumMz
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setMinSpectrumMz
Set the min spectrum m/z to search for.- Parameters:
minSpectrumMz
- the minSpectrumMz to set
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getMaxSpectrumMz
Returns the max spectrum m/z to search for.- Returns:
- the maxSpectrumMz
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setMaxSpectrumMz
Set the max spectrum m/z to search for.- Parameters:
maxSpectrumMz
- the maxSpectrumMz to set
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getMinSpectrumPeaks
Returns the min number of peaks in a spectrum.- Returns:
- the minSpectrumPeaks
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setMinSpectrumPeaks
Set the min number of peaks in a spectrum.- Parameters:
minSpectrumPeaks
- the minSpectrumPeaks to set
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getSpectrumCharges
Returns the spectrum charges to search for.- Returns:
- the spectrumCharges
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setSpectrumCharges
Set the spectrum charges to search for.- Parameters:
spectrumCharges
- the spectrumCharges to set
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getRemovePrecursor
Returns true of the precursor peak is to be removed.- Returns:
- the removePrecursor
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setRemovePrecursor
Set if the precursor peak is to be removed.- Parameters:
removePrecursor
- the removePrecursor to set
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getRemovePrecursorTolerance
Returns the tolerance with which to remove the precursor peak.- Returns:
- the removePrecursorTolerance
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setRemovePrecursorTolerance
Set the tolerance with which to remove the precursor peak.- Parameters:
removePrecursorTolerance
- the removePrecursorTolerance to set
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getPrintProgressIndicatorSize
Returns the progress indicator size.- Returns:
- the printProgressIndicatorSize
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setPrintProgressIndicatorSize
Set the progress indicator size.- Parameters:
printProgressIndicatorSize
- the printProgressIndicatorSize to set
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getUseFlankingPeaks
Returns true if flanking peaks are to be used.- Returns:
- the useFlankingPeaks
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setUseFlankingPeaks
Set if flanking peaks are to be used.- Parameters:
useFlankingPeaks
- the useFlankingPeaks to set
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getUseNeutralLossPeaks
Returns true if the neutral loss peaks are to be used.- Returns:
- the useNeutralLossPeaks
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setUseNeutralLossPeaks
Set if the neutral loss peaks are to be used.- Parameters:
useNeutralLossPeaks
- the useNeutralLossPeaks to set
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getMzBinWidth
Returns the m/z bin width.- Returns:
- the mzBinWidth
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setMzBinWidth
Set the m/z bin width.- Parameters:
mzBinWidth
- the mzBinWidth to set
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getMzBinOffset
Returns the m/z bin offset.- Returns:
- the mzBinOffset
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setMzBinOffset
Set the m/z bin offset.- Parameters:
mzBinOffset
- the mzBinOffset to set
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getConcatenatTargetDecoy
Returns true if the target and decoy results are to be concatenated.- Returns:
- the concatenatTargetDecoy
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setConcatenatTargetDecoy
Set if the target and decoy results are to be concatenated.- Parameters:
concatenate
- the concatenateTargetDecoy to set
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getStoreSpectraFileName
Returns the name of the file where the binary spectra are to be stored.- Returns:
- the storeSpectraFileName
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setStoreSpectraFileName
Set the name of the file where the binary spectra are to be stored.- Parameters:
storeSpectraFileName
- the storeSpectraFileName to set
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getTextOutput
Returns true if the text output is to be created.- Returns:
- the textOutput
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setTextOutput
Set if the text output is to be created.- Parameters:
textOutput
- the textOutput to set
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getSqtOutput
Returns true if the sqt output is to be created.- Returns:
- the sqtOutput
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setSqtOutput
Set if the sqt output is to be created.- Parameters:
sqtOutput
- the sqtOutput to set
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getPepXmlOutput
Returns true if the pepxml output is to be created.- Returns:
- the pepXmlOutput
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setPepXmlOutput
Set if the pepxml output is to be created.- Parameters:
pepXmlOutput
- the pepXmlOutput to set
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getMzidOutput
Returns true if the mzid output is to be created.- Returns:
- the mzidOutput
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setMzidOutput
Set if the mzid output is to be created.- Parameters:
mzidOutput
- the mzidOutput to set
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getPinOutput
Returns true if the Percolator output is to be created.- Returns:
- the pinOutput
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setPinOutput
Set if the Percolator output is to be created.- Parameters:
pinOutput
- the pinOutput to set
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getFastIndexFolderName
Returns the name of the FASTA index folder.- Returns:
- the fastIndexFolderName
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setFastIndexFolderName
Set the name of the FASTA index folder.- Parameters:
fastIndexFolderName
- the fastIndexFolderName to set
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getRemoveTempFolders
Returns true if the output and index folders are to be removed when the search has completed.- Returns:
- the removeTempFolders
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setRemoveTempFolders
Set if the output and index folders are to be removed when the search has completed.- Parameters:
removeTempFolders
- the removeTempFolders to set
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