java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
All Implemented Interfaces:
IdentificationAlgorithmParameter, Serializable

public class MsAmandaParameters
extends ExperimentObject
implements IdentificationAlgorithmParameter
The MS Amanda specific parameters.
Author:
Harald Barsnes
See Also:
Serialized Form
  • Field Details

  • Constructor Details

  • 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
    • generateDecoy

      public boolean generateDecoy()
      Returns whether a decoy database shall be created and searched against.
      Returns:
      true if a decoy database shall be created and searched against
    • setGenerateDecoyDatabase

      public void setGenerateDecoyDatabase​(boolean generateDecoy)
      Set whether a decoy database shall be created and searched against.
      Parameters:
      generateDecoy - the generateDecoy to set
    • isMonoIsotopic

      public boolean isMonoIsotopic()
      Returns whether monoisotopic mass values shall be used (in contrast to average mass values).
      Returns:
      true if mass values shall be used (in contrast to average mass values)
    • setMonoIsotopic

      public void setMonoIsotopic​(boolean monoisotopic)
      Set whether monoisotopic mass values shall be used (in contrast to average mass values).
      Parameters:
      monoisotopic - the monoisotopic to set
    • getInstrumentID

      public String getInstrumentID()
      Return the instrument ID.
      Returns:
      the instrument ID
    • setInstrumentID

      public void setInstrumentID​(String instrumentID)
      Set the instrument ID.
      Parameters:
      instrumentID - the instrument ID to set
    • getMaxRank

      public Integer getMaxRank()
      Returns the maximum rank.
      Returns:
      the max rank
    • setMaxRank

      public void setMaxRank​(Integer maxRank)
      Set the maximum rank.
      Parameters:
      maxRank - the maxRank to set
    • isLowMemoryMode

      public boolean isLowMemoryMode()
      Deprecated.
      use getMaxLoadedProteins and getMaxLoadedSpectra instead
      Returns whether the low memory mode is used.
      Returns:
      true if in low memory mode
    • setLowMemoryMode

      public void setLowMemoryMode​(boolean lowMemoryMode)
      Deprecated.
      use setMaxLoadedProteins and setMaxLoadedSpectra instead
      Set whether the low memory mode is used.
      Parameters:
      lowMemoryMode - the low memory mode to set
    • isPerformDeisotoping

      public boolean isPerformDeisotoping()
      Returns whether deisotoping is to be performed.
      Returns:
      true if deisotoping is to be performed
    • setPerformDeisotoping

      public void setPerformDeisotoping​(boolean performDeisotoping)
      Sets if deisotoping is to be performed.
      Parameters:
      performDeisotoping - the performDeisotoping to set
    • getMaxModifications

      public Integer getMaxModifications()
      Returns the maximum number of modifications per peptide.
      Returns:
      the maximum number of modifications
    • setMaxModifications

      public void setMaxModifications​(Integer maxModifications)
      Set the maximum number of modifications per peptide.
      Parameters:
      maxModifications - the maximum number of modifications
    • getMaxVariableModifications

      public Integer getMaxVariableModifications()
      Returns the maximum number of variable modifications per peptide.
      Returns:
      the maximum number of variable modifications
    • setMaxVariableModifications

      public void setMaxVariableModifications​(Integer maxVariableModifications)
      Set the maximum number of variable modifications per peptide.
      Parameters:
      maxVariableModifications - the maximum number of variable modifications
    • getMaxModificationSites

      public Integer getMaxModificationSites()
      Returns the maximum number of modifications sites per modification per peptide.
      Returns:
      the maximum number of modifications sites per modification per peptide
    • setMaxModificationSites

      public void setMaxModificationSites​(Integer maxModificationSites)
      Set the maximum number of modifications sites per modification per peptide.
      Parameters:
      maxModificationSites - the maximum number of modifications sites per modification per peptide
    • getMaxNeutralLosses

      public Integer getMaxNeutralLosses()
      Returns the maximum number of water and ammonia losses per peptide.
      Returns:
      the maximum number of water and ammonia losses per peptide
    • setMaxNeutralLosses

      public void setMaxNeutralLosses​(Integer maxNeutralLosses)
      Set the maximum number of water and ammonia losses per peptide.
      Parameters:
      maxNeutralLosses - the maximum number of water and ammonia losses per peptide
    • getMaxNeutralLossesPerModification

      public Integer getMaxNeutralLossesPerModification()
      Returns the maximum number identical modification specific losses per peptide.
      Returns:
      the the maximum number identical modification specific losses per peptide
    • setMaxNeutralLossesPerModification

      public void setMaxNeutralLossesPerModification​(Integer maxNeutralLossesPerModification)
      Set the maximum number identical modification specific losses per peptide.
      Parameters:
      maxNeutralLossesPerModification - the maximum number identical modification specific losses per peptide
    • getMinPeptideLength

      public Integer getMinPeptideLength()
      Returns the minimum peptide length.
      Returns:
      the the minimum peptide length
    • setMinPeptideLength

      public void setMinPeptideLength​(Integer minPeptideLength)
      Set the minimum peptide length.
      Parameters:
      minPeptideLength - the minimum peptide length
    • getMaxPeptideLength

      public Integer getMaxPeptideLength()
      Returns the maximum peptide length.
      Returns:
      the the maximum peptide length
    • setMaxPeptideLength

      public void setMaxPeptideLength​(Integer maxPeptideLength)
      Set the maximum peptide length.
      Parameters:
      maxPeptideLength - the maximum peptide length
    • getMaxLoadedProteins

      public Integer getMaxLoadedProteins()
      Returns the maximum number of proteins loaded into memory.
      Returns:
      the maximum number of proteins loaded into memory
    • setMaxLoadedProteins

      public void setMaxLoadedProteins​(Integer maxLoadedProteins)
      Set the maximum number of proteins loaded into memory.
      Parameters:
      maxLoadedProteins - the maximum number of proteins loaded into memory
    • getMaxLoadedSpectra

      public Integer getMaxLoadedSpectra()
      Returns the maximum number of spectra loaded into memory.
      Returns:
      the maximum number of spectra loaded into memory
    • setMaxLoadedSpectra

      public void setMaxLoadedSpectra​(Integer maxLoadedSpectra)
      Set the maximum number of spectra loaded into memory.
      Parameters:
      maxLoadedSpectra - the maximum number of spectra loaded into memory
    • 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
    • reportBothBestHitsForTD

      public boolean reportBothBestHitsForTD()
      Returns true if target and decoy are ranked separately, false if shared rank.
      Returns:
      true if target and decoy are ranked separately, false if shared rank
    • setReportBothBestHitsForTD

      public void setReportBothBestHitsForTD​(boolean reportBothBestHitsForTD)
      Set if target and decoy are ranked separately or shared.
      Parameters:
      reportBothBestHitsForTD - the reportBothBestHitsForTD to set