TideParameters (computational omics utilities 4.5.7 API)

java.lang.Object
- com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters

All Implemented Interfaces:

IdentificationAlgorithmParameter, Serializable
```
public class TideParameters
extends Object
implements IdentificationAlgorithmParameter
```
The Tide specific parameters.

Author:

Harald Barsnes

See Also:

Serialized Form

Constructor Summary

Constructors
Constructor and Description

TideParameters()
Constructor.

Constructors
Constructor and Description
`TideParameters()` Constructor.

Method Summary

All Methods Instance Methods Concrete 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.
`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`	`getMaxVariablePtmsPerPeptide()` Returns the maximum number of variable modifications allowed on a single peptide.
`Integer`	`getMaxVariablePtmsPerTypePerPeptide()` 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 decoys
`void`	`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`	`setMaxVariablePtmsPerPeptide(Integer maxVariablePtmsPerPeptide)` Set the maximum number of variable modifications of allowed on a single peptide.
`void`	`setMaxVariablePtmsPerTypePerPeptide(Integer maxVariablePtmsPerTypePerPeptide)` 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 java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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

Class TideParameters

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

TideParameters

Method Detail

getAlgorithm

equals

toString

getMaxVariablePtmsPerPeptide

setMaxVariablePtmsPerPeptide

getMaxVariablePtmsPerTypePerPeptide

setMaxVariablePtmsPerTypePerPeptide

getMaxPeptideLength

setMaxPeptideLength

getMinPeptideLength

setMinPeptideLength

getMinPrecursorMass

setMinPrecursorMass

getMaxPrecursorMass

setMaxPrecursorMass

getDecoyFormat

setDecoyFormat

getKeepTerminalAminoAcids

setKeepTerminalAminoAcids

getDecoySeed

setDecoySeed

getOutputFolderName

setOutputFolderName

getPrintPeptides

setPrintPeptides

getVerbosity

setVerbosity

getMonoisotopicPrecursor

setMonoisotopicPrecursor

getClipNtermMethionine

setClipNtermMethionine

getDigestionType

setDigestionType

getComputeSpScore

setComputeSpScore

getNumberOfSpectrumMatches

setNumberOfSpectrumMatches

getComputeExactPValues

setComputeExactPValues

getMinSpectrumMz

setMinSpectrumMz

getMaxSpectrumMz

setMaxSpectrumMz

getMinSpectrumPeaks

setMinSpectrumPeaks

getSpectrumCharges

setSpectrumCharges

getRemovePrecursor

setRemovePrecursor

getRemovePrecursorTolerance

setRemovePrecursorTolerance

getPrintProgressIndicatorSize

setPrintProgressIndicatorSize

getUseFlankingPeaks

setUseFlankingPeaks

getUseNeutralLossPeaks

setUseNeutralLossPeaks

getMzBinWidth

setMzBinWidth

getMzBinOffset

setMzBinOffset

getConcatenatTargetDecoy

setConcatenatTargetDecoy

getStoreSpectraFileName

setStoreSpectraFileName

getTextOutput

setTextOutput

getSqtOutput

setSqtOutput

getPepXmlOutput

setPepXmlOutput

getMzidOutput

setMzidOutput