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

Class MyriMatchParameters

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

  • Constructor Details

    • MyriMatchParameters

      public MyriMatchParameters()
      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(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

    • getNumberOfSpectrumMatches

      public Integer getNumberOfSpectrumMatches()
      Returns the maximum number of spectrum matches.
      Returns:
      the numberOfSpectrumMarches

    • setNumberOfSpectrumMatches

      public void setNumberOfSpectrumMatches(Integer numberOfSpectrumMarches)
      Set the maximum number of spectrum matches.
      Parameters:
      numberOfSpectrumMarches - the numberOfSpectrumMarches to set

    • getTicCutoffPercentage

      public Double getTicCutoffPercentage()
      Returns the TicCutoffPercentage.
      Returns:
      the ticCutoffPercentage

    • setTicCutoffPercentage

      public void setTicCutoffPercentage(Double ticCutoffPercentage)
      Set the TicCutoffPercentage.
      Parameters:
      ticCutoffPercentage - the ticCutoffPercentage to set

    • getMaxDynamicMods

      public Integer getMaxDynamicMods()
      Returns the maximum number of variable modifications.
      Returns:
      the maxDynamicMods

    • setMaxDynamicMods

      public void setMaxDynamicMods(Integer maxDynamicMods)
      Set the maximum number of variable modifications.
      Parameters:
      maxDynamicMods - the maxDynamicMods to set

    • getMinTerminiCleavages

      public Integer getMinTerminiCleavages()
      Returns the minimum number of termini cleavages.
      Returns:
      the maxDynamicMods

    • setMinTerminiCleavages

      public void setMinTerminiCleavages(Integer minTerminiCleavages)
      Set the minimum number of termini cleavages.
      Parameters:
      minTerminiCleavages - the minTerminiCleavages to set

    • 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

    • getUseSmartPlusThreeModel

      public boolean getUseSmartPlusThreeModel()
      Returns true if the UseSmartPlusThreeModel is to be used.
      Returns:
      true if the UseSmartPlusThreeModel is to be used

    • setUseSmartPlusThreeModel

      public void setUseSmartPlusThreeModel(boolean useSmartPlusThreeModel)
      Sets if the UseSmartPlusThreeModel is to be used.
      Parameters:
      useSmartPlusThreeModel - if the UseSmartPlusThreeModel is to be used

    • getComputeXCorr

      public boolean getComputeXCorr()
      Returns true if a Sequest-like cross correlation score will be calculated for the top ranking hits in each spectrum’s result set.
      Returns:
      true if the Sequest-like cross correlation score is to be calculated

    • setComputeXCorr

      public void setComputeXCorr(boolean computeXCorr)
      Sets if a Sequest-like cross correlation score will be calculated for the top ranking hits in each spectrum’s result set.
      Parameters:
      computeXCorr - if the Sequest-like cross correlation score is to be calculated

    • getNumIntensityClasses

      public Integer getNumIntensityClasses()
      Returns the number of intensity classes.
      Returns:
      the number of intensity classes

    • setNumIntensityClasses

      public void setNumIntensityClasses(Integer numIntensityClasses)
      Set the number of intensity classes.
      Parameters:
      numIntensityClasses - he number of intensity classes

    • getClassSizeMultiplier

      public Integer getClassSizeMultiplier()
      Returns the intensity class size multiplier.
      Returns:
      the intensity class size multiplier

    • setClassSizeMultiplier

      public void setClassSizeMultiplier(Integer classSizeMultiplier)
      Set the intensity class size multiplier.
      Parameters:
      classSizeMultiplier - the intensity class size multiplier

    • getNumberOfBatches

      public Integer getNumberOfBatches()
      Set the number of batches per node to strive for when using the MPI-based parallelization features.
      Returns:
      the number of batches per node

    • setNumberOfBatches

      public void setNumberOfBatches(Integer numberOfBatches)
      Set the number of batches per node to strive for when using the MPI-based parallelization features.
      Parameters:
      numberOfBatches - the number of batches per node

    • getFragmentationRule

      public String getFragmentationRule()
      Returns the fragmentation rule.
      Returns:
      the fragmentation rule

    • setFragmentationRule

      public void setFragmentationRule(String fragmentationRule)
      Set the fragmentation rule.
      Parameters:
      fragmentationRule - the fragmentation rule

    • getMaxPeakCount

      public Integer getMaxPeakCount()
      Returns the max peak count.
      Returns:
      the max peak count

    • setMaxPeakCount

      public void setMaxPeakCount(Integer maxPeakCount)
      Set the max peak count.
      Parameters:
      maxPeakCount - the max peak count

    • getOutputFormat

      public String getOutputFormat()
      Returns the output format.
      Returns:
      the outputFormat

    • setOutputFormat

      public void setOutputFormat(String outputFormat)
      Set the output format.
      Parameters:
      outputFormat - the outputFormat to set

    • enzymeMapping

      public static String enzymeMapping(DigestionParameters digestionPreferences)
      Tries to map the utilities enzyme in the digestion preferences to the enzymes supported by MyriMatch.
      Parameters:
      digestionPreferences - the digestion preferences
      Returns:
      the MyriMatch enzyme as a string, or null of no mapping is found