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

Class SageParameters

java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.tool_specific.SageParameters
All Implemented Interfaces:
IdentificationAlgorithmParameter, Serializable
public class SageParameters extends ExperimentObject implements IdentificationAlgorithmParameter
The Sage specific parameters.
Author:
Harald Barsnes
See Also:

  • Constructor Details

    • SageParameters

      public SageParameters()
      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

    • getMaxPeptideLength

      public Integer getMaxPeptideLength()
      Returns the maximal peptide length allowed.
      Returns:
      the maximal peptide length allowed

    • setMaxPeptideLength

      public void setMaxPeptideLength(int 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(int minPeptideLength)
      Sets the minimal peptide length allowed.
      Parameters:
      minPeptideLength - the minimal peptide length allowed

    • getBucketSize

      public Integer getBucketSize()
      Returns the bucket size.
      Returns:
      the bucketSize

    • setBucketSize

      public void setBucketSize(Integer bucketSize)
      Set the bucket size.
      Parameters:
      bucketSize - the bucketSize to set

    • getMinFragmentMz

      public Double getMinFragmentMz()
      Returns the minimum fragment mz.
      Returns:
      the minFragmentMz

    • setMinFragmentMz

      public void setMinFragmentMz(Double minFragmentMz)
      Set the minimum fragment mz.
      Parameters:
      minFragmentMz - the minFragmentMz to set

    • getMaxFragmentMz

      public Double getMaxFragmentMz()
      Returns the maximum fragment mz.
      Returns:
      the maxFragmentMz

    • setMaxFragmentMz

      public void setMaxFragmentMz(Double maxFragmentMz)
      Set the maximum fragment mz.
      Parameters:
      maxFragmentMz - the maxFragmentMz to set

    • getMinPeptideMass

      public Double getMinPeptideMass()
      Returns the minimum peptide mass.
      Returns:
      the minPeptideMass

    • setMinPeptideMass

      public void setMinPeptideMass(Double minPeptideMass)
      Set the minimum peptide mass.
      Parameters:
      minPeptideMass - the minPeptideMass to set

    • getMaxPeptideMass

      public Double getMaxPeptideMass()
      Returns the maximum peptide mass.
      Returns:
      the maxPeptideMass

    • setMaxPeptideMass

      public void setMaxPeptideMass(Double maxPeptideMass)
      Set the maximum peptide mass.
      Parameters:
      maxPeptideMass - the maxPeptideMass to set

    • getMinIonIndex

      public Integer getMinIonIndex()
      Returns the minimm ion index.
      Returns:
      the minIonIndex

    • setMinIonIndex

      public void setMinIonIndex(Integer minIonIndex)
      Sets the minimum ion index.
      Parameters:
      minIonIndex - the minIonIndex to set

    • getDecoyTag

      public String getDecoyTag()
      Deprecated.
      use the decoy tag from FastaParameters instead
      Returns the decoy tag, null if not set.
      Returns:
      the decoyTag

    • setDecoyTag

      public void setDecoyTag(String decoyTag)
      Deprecated.
      use the decoy tag from FastaParameters instead
      Set the decoy tag, null if no decoy tag is used.
      Parameters:
      decoyTag - the decoyTag to set

    • getGenerateDecoys

      public Boolean getGenerateDecoys()
      Returns true if decoys are to be generated.
      Returns:
      true if decoys are to be generated

    • setGenerateDecoys

      public void setGenerateDecoys(Boolean generateDecoys)
      Set whether decoys are to be generated.
      Parameters:
      generateDecoys - the generateDecoys to set

    • getTmtType

      public String getTmtType()
      Returns the TMT type.
      Returns:
      the TMT type

    • setTmtType

      public void setTmtType(String tmtType)
      Sets the TMT type.
      Parameters:
      tmtType - the TMT type to set

    • getTmtLevel

      public Integer getTmtLevel()
      Returns the TMT level.
      Returns:
      the TMT level

    • setTmtLevel

      public void setTmtLevel(Integer tmtLevel)
      Sets the TMT level.
      Parameters:
      tmtLevel - the TMT level to set

    • getTmtSn

      public Boolean getTmtSn()
      Returns true if Signal/Noise should be used instead of intensity for TMT quantification.
      Returns:
      true if Signal/Noise should be used instead of intensity for TMT quantification

    • setTmtSn

      public void setTmtSn(Boolean tmtSn)
      Set if Signal/Noise should be used instead of intensity for TMT quantification.
      Parameters:
      tmtSn - the tmtSn to set

    • getPerformLfq

      public Boolean getPerformLfq()
      Returns true if LFQ is to be performed.
      Returns:
      true if LFQ is to be performed

    • setPerformLfq

      public void setPerformLfq(Boolean performLfq)
      Set if LFQ is to be performed.
      Parameters:
      performLfq - the performLfq to set

    • getDeisotope

      public Boolean getDeisotope()
      Returns true if deisotoping is to be performed.
      Returns:
      true if deisotoping is to be performed

    • setDeisotope

      public void setDeisotope(Boolean deisotope)
      Set whether deisotoping is to be performed.
      Parameters:
      deisotope - the deisotope to set

    • getChimera

      public Boolean getChimera()
      Returns true if chimeric spectra are to be considered.
      Returns:
      true if chimeric spectra are to be considered

    • setChimera

      public void setChimera(Boolean chimera)
      Set whether chimeric spectra are to be considered.
      Parameters:
      chimera - the chimera to set

    • getWideWindow

      public Boolean getWideWindow()
      Returns true if wide windows are to be used.
      Returns:
      true if wide windows are to be used

    • setWideWindow

      public void setWideWindow(Boolean wideWindow)
      Set whether wide windows are to be used.
      Parameters:
      wideWindow - the wide window to set

    • getPredictRt

      public Boolean getPredictRt()
      Returns true if RT is to be predicted.
      Returns:
      true if RT is to be predicted

    • setPredictRt

      public void setPredictRt(Boolean predictRt)
      Set whether RT is to be predicted.
      Parameters:
      predictRt - the predictRt to set

    • getMinPeaks

      public Integer getMinPeaks()
      Returns the minimum number of peaks required.
      Returns:
      the minPeaks

    • setMinPeaks

      public void setMinPeaks(Integer minPeaks)
      Set the minimum number of peaks required.
      Parameters:
      minPeaks - the minPeaks to set

    • getMaxPeaks

      public Integer getMaxPeaks()
      Returns the maximum number of peaks required.
      Returns:
      the maxPeaks

    • setMaxPeaks

      public void setMaxPeaks(Integer maxPeaks)
      Set the maximum number of peaks required.
      Parameters:
      maxPeaks - the maxPeaks to set

    • getMinMatchedPeaks

      public Integer getMinMatchedPeaks()
      Returns the minimum number of matched b+y ions to use for reporting PSMs.
      Returns:
      the minimum number of matched b+y ions

    • setMinMatchedPeaks

      public void setMinMatchedPeaks(Integer minMatchedPeaks)
      Set the minimum number of matched b+y ions to use for reporting PSMs.
      Parameters:
      minMatchedPeaks - the minMatchedPeaks to set

    • getMaxFragmentCharge

      public Integer getMaxFragmentCharge()
      Returns the maximum fragment charge.
      Returns:
      the maxFragmentCharge

    • setMaxFragmentCharge

      public void setMaxFragmentCharge(Integer maxFragmentCharge)
      Set the maximum fragment charge.
      Parameters:
      maxFragmentCharge - the maxFragmentCharge to set

    • getNumPsmsPerSpectrum

      public Integer getNumPsmsPerSpectrum()
      Returns the number of PSMs per spectrum.
      Returns:
      the numPsmsPerSpectrum

    • setNumPsmsPerSpectrum

      public void setNumPsmsPerSpectrum(Integer numPsmsPerSpectrum)
      Set the number of PSMs per spectrum.
      Parameters:
      numPsmsPerSpectrum - the numPsmsPerSpectrum to set

    • getBatchSize

      public Integer getBatchSize()
      Returns the batch size. Null if not set.
      Returns:
      the batch size

    • setBatchSize

      public void setBatchSize(Integer batchSize)
      Set the batch size.
      Parameters:
      batchSize - the batch size to set

    • getMaxVariableMods

      public Integer getMaxVariableMods()
      Returns the maximum variable modifications per peptide.
      Returns:
      the maxVariableMods

    • setMaxVariableMods

      public void setMaxVariableMods(Integer maxVariableMods)
      Set the maximum variable modifications per peptide.
      Parameters:
      maxVariableMods - the maxVariableMods to set

    • getLfqPeakScoring

      public String getLfqPeakScoring()
      Returns the LFQ peak scoring method.
      Returns:
      the lfqPeakScoring

    • setLfqPeakScoring

      public void setLfqPeakScoring(String lfqPeakScoring)
      Sets the LFQ peak scoring method.
      Parameters:
      lfqPeakScoring - the lfqPeakScoring to set

    • getLfqIntergration

      public String getLfqIntergration()
      Returns the LFQ integration type.
      Returns:
      the lfqIntergration

    • setLfqIntergration

      public void setLfqIntergration(String lfqIntergration)
      Sets the LFQ integration type.
      Parameters:
      lfqIntergration - the lfqIntergration to set

    • getLfqSpectralAngle

      public Double getLfqSpectralAngle()
      Returns the LFQ spectral angel.
      Returns:
      the lfqSpectralAngle

    • setLfqSpectralAngle

      public void setLfqSpectralAngle(Double lfqSpectralAngle)
      Set the LFQ spectral angel.
      Parameters:
      lfqSpectralAngle - the lfqSpectralAngle to set

    • getLfqPpmTolerance

      public Double getLfqPpmTolerance()
      Returns the LFQ PPM tolerance.
      Returns:
      the lfqPpmTolerance

    • setLfqPpmTolerance

      public void setLfqPpmTolerance(Double lfqPpmTolerance)
      Sets the LFQ PPM tolerance.
      Parameters:
      lfqPpmTolerance - the lfqPpmTolerance to set

    • getCombineChargeStates

      public Boolean getCombineChargeStates()
      Returns true if the charge states are to be combined.
      Returns:
      true if the charge states are to be combined

    • setCombineChargeStates

      public void setCombineChargeStates(Boolean combineChargeStates)
      Sets whether the charge states are to be combined.
      Parameters:
      combineChargeStates - whether the charge states are to be combined