Package com.compomics.util.parameters.identification.tool_specific

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:

  • Constructor Details

    • TideParameters

      public TideParameters()
      Constructor.

  • Method Details

    • 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

    • getMaxVariableModificationsPerPeptide

      public Integer getMaxVariableModificationsPerPeptide()
      Returns the maximum number of variable modifications allowed on a single peptide. Null if no upper limit is set.
      Returns:
      the maxVariableModificationsPerPeptide

    • setMaxVariableModificationsPerPeptide

      public void setMaxVariableModificationsPerPeptide(Integer maxVariableModificationsPerPeptide)
      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

    • getMaxVariableModificationsPerTypePerPeptide

      public Integer 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

    • 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

    • 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()
      Deprecated.
      Removed in Tide 4.2 (or earlier)
      Returns the spectrum charges to search for.
      Returns:
      the spectrumCharges

    • setSpectrumCharges

      public void setSpectrumCharges(String spectrumCharges)
      Deprecated.
      Removed in Tide 4.2 (or earlier)
      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