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

Class MsgfParameters

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

  • Constructor Details

    • MsgfParameters

      public MsgfParameters()
      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

    • searchDecoyDatabase

      public boolean searchDecoyDatabase()
      Returns whether MS-GF+ is to create and search a decoy database.
      Returns:
      whether MS-GF+ is to create and search a decoy database

    • setSearchDecoyDatabase

      public void setSearchDecoyDatabase(boolean searchDecoyDatabase)
      Set whether MS-GF+ is to create and search a decoy database.
      Parameters:
      searchDecoyDatabase - the searchDecoyDatabase 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

    • getInstrumentID

      public int getInstrumentID()
      Return the instrument ID.
      Returns:
      the instrumentID

    • setInstrumentID

      public void setInstrumentID(int instrumentID)
      Set the instrument ID.
      Parameters:
      instrumentID - the instrumentID to set

    • getFragmentationType

      public int getFragmentationType()
      Return the fragmentation ID.
      Returns:
      the fragmentationType

    • setFragmentationType

      public void setFragmentationType(int fragmentationType)
      Set the fragmentation ID.
      Parameters:
      fragmentationType - the fragmentationType to set

    • getProtocol

      public int getProtocol()
      Returns the protocol ID.
      Returns:
      the protocol

    • setProtocol

      public void setProtocol(int protocol)
      Set the protocol ID.
      Parameters:
      protocol - the protocol to set

    • getNumberOfSpectrumMatches

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

    • setNumberOfSpectrumMarches

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

    • isAdditionalOutput

      public boolean isAdditionalOutput()
      Returns if additional output is to be included.
      Returns:
      the additionalOutput

    • setAdditionalOutput

      public void setAdditionalOutput(boolean additionalOutput)
      Set if additional output is to be included.
      Parameters:
      additionalOutput - the additionalOutput to set

    • getNumberTolerableTermini

      public Integer getNumberTolerableTermini()
      Returns the number of tolerable termini.
      Returns:
      the numberTolerableTermini

    • setNumberTolerableTermini

      public void setNumberTolerableTermini(Integer numberTolerableTermini)
      Set the number of tolerable termini.
      Parameters:
      numberTolerableTermini - the numberTolerableTermini to set

    • getNumberOfModificationsPerPeptide

      public Integer getNumberOfModificationsPerPeptide()
      Returns the maximum number of modifications per peptide.
      Returns:
      the maximum number of modifications per peptide

    • setNumberOfModificationsPerPeptide

      public void setNumberOfModificationsPerPeptide(Integer numberOfModificationsPerPeptide)
      Set the maximum number of modifications per peptide.
      Parameters:
      numberOfModificationsPerPeptide - the maximum number of modifications per peptide

    • getNumberOfTasks

      public Integer getNumberOfTasks()
      Returns the number of tasks, null if not set.
      Returns:
      the number of tasks

    • setNumberOfTasks

      public void setNumberOfTasks(Integer numberOfTasks)
      Set the number of tasks. Set to null to leave the choice to MS-GF+.
      Parameters:
      numberOfTasks - the number of tasks