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

Class MsAmandaParameters

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:

  • Field Details

    • MAX_MS_AMANDA_FASTA_FILE_NAME_LENGTH

      public static final int MAX_MS_AMANDA_FASTA_FILE_NAME_LENGTH
      The maximum allowed length of the FASTA file name.
      See Also:

  • Constructor Details

    • MsAmandaParameters

      public MsAmandaParameters()
      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

    • 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

    • getMaxAllowedChargeState

      public String getMaxAllowedChargeState()
      Returns the maximum allowed charge state.
      Returns:
      the maximum allowed charge state

    • setMaxAllowedChargeState

      public void setMaxAllowedChargeState(String maxAllowedChargeState)
      Set the maximum allowed charge state.
      Parameters:
      maxAllowedChargeState - the max allowed charge state

    • getMinPeakDepth

      public Integer getMinPeakDepth()
      Returns the minimum peak depth.
      Returns:
      the minimum peak depth

    • setMinPeakDepth

      public void setMinPeakDepth(Integer minPeakDepth)
      Set the minimum peak depth.
      Parameters:
      minPeakDepth - the minimum peak depth

    • getMaxPeakDepth

      public Integer getMaxPeakDepth()
      Returns the maximum peak depth.
      Returns:
      the maximum peak depth

    • setMaxPeakDepth

      public void setMaxPeakDepth(Integer maxPeakDepth)
      Set the maximum peak depth.
      Parameters:
      maxPeakDepth - the maximum peak depth

    • getPerformSecondSearch

      public Boolean getPerformSecondSearch()
      Returns true if a second search is to be performed.
      Returns:
      true if a second search is to be performed

    • setPerformSecondSearch

      public void setPerformSecondSearch(Boolean performSecondSearch)
      Set if a second search is to be performed.
      Parameters:
      performSecondSearch - whether a second search is to be performed

    • getKeepY1Ion

      public Boolean getKeepY1Ion()
      Returns true if the Y1 ions are to be kept.
      Returns:
      true if the Y1 ions are to be kept

    • setKeepY1Ion

      public void setKeepY1Ion(Boolean keepY1Ion)
      Set whether the Y1 ions are to be kept.
      Parameters:
      keepY1Ion - whether the Y1 ions are to be kept

    • getRemoveWaterLosses

      public Boolean getRemoveWaterLosses()
      Returns true if the water losses are to be removed.
      Returns:
      true if the water losses are to be removed

    • setRemoveWaterLosses

      public void setRemoveWaterLosses(Boolean removeWaterLosses)
      Set whether the water losses are to be removed.
      Parameters:
      removeWaterLosses - whether the water losses are to be removed

    • getRemoveAmmoniaLosses

      public Boolean getRemoveAmmoniaLosses()
      Returns true if the ammonia losses are to be removed.
      Returns:
      the removeAmmoniaLosses

    • setRemoveAmmoniaLosses

      public void setRemoveAmmoniaLosses(Boolean removeAmmoniaLosses)
      Set whether the ammonia losses are to be removed.
      Parameters:
      removeAmmoniaLosses - whether the ammonia losses are to be removed

    • getExcludeFirstPrecursor

      public Boolean getExcludeFirstPrecursor()
      Returns true if the first precursor is to be excluded.
      Returns:
      true if the first precursor is to be excluded

    • setExcludeFirstPrecursor

      public void setExcludeFirstPrecursor(Boolean excludeFirstPrecursor)
      Set whether the first precursor is to be excluded.
      Parameters:
      excludeFirstPrecursor - whether the first precursor is to be excluded

    • getMaxMultiplePrecursors

      public Integer getMaxMultiplePrecursors()
      Returns the maximum number of precursors.
      Returns:
      the maximum number of precursors

    • setMaxMultiplePrecursors

      public void setMaxMultiplePrecursors(Integer maxMultiplePrecursors)
      Set the maximum number of precursors.
      Parameters:
      maxMultiplePrecursors - the maximum number of precursors

    • getConsideredChargesForPrecursors

      public String getConsideredChargesForPrecursors()
      Returns the considered charges for precursors.
      Returns:
      the considered charges for precursors

    • setConsideredChargesForPrecursors

      public void setConsideredChargesForPrecursors(String consideredChargesForPrecursors)
      Set the considered charges for precursors.
      Parameters:
      consideredChargesForPrecursors - the considered charges for precursors

    • getCombineConsideredCharges

      public Boolean getCombineConsideredCharges()
      Returns true if considered charges are combined in one result.
      Returns:
      true if considered charges are combined in one result

    • setCombineConsideredCharges

      public void setCombineConsideredCharges(Boolean combineConsideredCharges)
      Set if considered charges are combined in one result.
      Parameters:
      combineConsideredCharges - combine considered charges in one result

    • getRunPercolator

      public Boolean getRunPercolator()
      Returns true if Percolator is to be run.
      Returns:
      true if Percolator is to be run

    • setRunPercolator

      public void setRunPercolator(Boolean runPercolator)
      Set if Percolator is to be run.
      Parameters:
      runPercolator - if Percolator is to be run

    • getGeneratePInFile

      public Boolean getGeneratePInFile()
      Returns true if a PIn file is to be generated.
      Returns:
      true if a PIn file is to be generated

    • setGeneratePInFile

      public void setGeneratePInFile(Boolean generatePInFile)
      Set whether a PIn file is to be generated.
      Parameters:
      generatePInFile - hether a PIn file is to be generated