org.proteios.io
Class XTandemParameterSet

java.lang.Object
  org.proteios.io.XTandemParameterSet

public class XTandemParameterSet
extends Object

This file API should be used to get parameter data from XTandem input files.

Author:

olle

Constructor Summary

XTandemParameterSet()

Method Summary

String	getListPathDefaultParameters()
String	getListPathTaxonomyInformation()
String	getOutputHistogramColumnWidth()
String	getOutputHistograms()
String	getOutputLogPath()
String	getOutputMaximumValidExpectationValue()
String	getOutputMessage()
String	getOutputOneSequenceCopy()
String	getOutputParameters()
String	getOutputPath()
String	getOutputPathHashing()
String	getOutputPerformance()
String	getOutputProteins()
String	getOutputResults()
String	getOutputSequencePath()
String	getOutputSequences()
String	getOutputSortResultsBy()
String	getOutputSpectra()
String	getOutputXslPath()
String	getProteinCleavageCTerminalMassChange()
String	getProteinCleavageNTerminalMassChange()
String	getProteinCleavageSite()
String	getProteinCTerminalResidueModificationMass()
String	getProteinHomologManagement()
String	getProteinModifiedResidueMassFile()
String	getProteinNTerminalResidueModificationMass()
String	getProteinTaxon()
String	getRefine()
String	getRefineMaximumValidExpectationValue()
String	getRefineModificationMass()
String	getRefinePointMutations()
String	getRefinePotentialCTerminusModifications()
String	getRefinePotentialModificationMass()
String	getRefinePotentialModificationMotif()
String	getRefinePotentialNTerminusModifications()
String	getRefineSequencePath()
String	getRefineSpectrumSynthesis()
String	getRefineTicPercent()
String	getRefineUnanticipatedCleavage()
String	getRefineUsePotentialModificationsForFullRefinement()
String	getResidueModificationMass()
String	getResiduePotentialModificationMass()
String	getResiduePotentialModificationMotif()
String	getScoringAIons()
String	getScoringAlgorithm()
String	getScoringBIons()
String	getScoringCIons()
String	getScoringCyclicPermutation()
String	getScoringIncludeReverse()
String	getScoringMaximumMissedCleavageSites()
String	getScoringMinimumIonCount()
String	getScoringXIons()
String	getScoringYIons()
String	getScoringZIons()
String	getSpectrumDynamicRange()
String	getSpectrumFragmentMassType()
String	getSpectrumFragmentMonoisotopicMassError()
String	getSpectrumFragmentMonoisotopicMassErrorUnits()
String	getSpectrumMaximumParentCharge()
String	getSpectrumMaximumParentMPlusH()
String	getSpectrumMinimumFragmentMz()
String	getSpectrumMinimumParentMPlusH()
String	getSpectrumMinimumPeaks()
String	getSpectrumParentMonoisotopicMassErrorMinus()
String	getSpectrumParentMonoisotopicMassErrorPlus()
String	getSpectrumParentMonoisotopicMassErrorUnits()
String	getSpectrumParentMonoisotopicMassIsotopeError()
String	getSpectrumPath()
String	getSpectrumSequenceBatchSize()
String	getSpectrumThreads()
String	getSpectrumTotalPeaks()
String	getSpectrumUseConditioning()
String	getSpectrumUseNoiseSuppression()
void	setListPathDefaultParameters(String listPathDefaultParameters)
void	setListPathTaxonomyInformation(String listPathTaxonomyInformation)
void	setOutputHistogramColumnWidth(String outputHistogramColumnWidth)
void	setOutputHistograms(String outputHistograms)
void	setOutputLogPath(String outputLogPath)
void	setOutputMaximumValidExpectationValue(String outputMaximumValidExpectationValue)
void	setOutputMessage(String outputMessage)
void	setOutputOneSequenceCopy(String outputOneSequenceCopy)
void	setOutputParameters(String outputParameters)
void	setOutputPath(String outputPath)
void	setOutputPathHashing(String outputPathHashing)
void	setOutputPerformance(String outputPerformance)
void	setOutputProteins(String outputProteins)
void	setOutputResults(String outputResults)
void	setOutputSequencePath(String outputSequencePath)
void	setOutputSequences(String outputSequences)
void	setOutputSortResultsBy(String outputSortResultsBy)
void	setOutputSpectra(String outputSpectra)
void	setOutputXslPath(String outputXslPath)
void	setProteinCleavageCTerminalMassChange(String proteinCleavageCTerminalMassChange)
void	setProteinCleavageNTerminalMassChange(String proteinCleavageNTerminalMassChange)
void	setProteinCleavageSite(String proteinCleavageSite)
void	setProteinCTerminalResidueModificationMass(String proteinCTerminalResidueModificationMass)
void	setProteinHomologManagement(String proteinHomologManagement)
void	setProteinModifiedResidueMassFile(String proteinModifiedResidueMassFile)
void	setProteinNTerminalResidueModificationMass(String proteinNTerminalResidueModificationMass)
void	setProteinTaxon(String proteinTaxon)
void	setRefine(String refine)
void	setRefineMaximumValidExpectationValue(String refineMaximumValidExpectationValue)
void	setRefineModificationMass(String refineModificationMass)
void	setRefinePointMutations(String refinePointMutations)
void	setRefinePotentialCTerminusModifications(String refinePotentialCTerminusModifications)
void	setRefinePotentialModificationMass(String refinePotentialModificationMass)
void	setRefinePotentialModificationMotif(String refinePotentialModificationMotif)
void	setRefinePotentialNTerminusModifications(String refinePotentialNTerminusModifications)
void	setRefineSequencePath(String refineSequencePath)
void	setRefineSpectrumSynthesis(String refineSpectrumSynthesis)
void	setRefineTicPercent(String refineTicPercent)
void	setRefineUnanticipatedCleavage(String refineUnanticipatedCleavage)
void	setRefineUsePotentialModificationsForFullRefinement(String refineUsePotentialModificationsForFullRefinement)
void	setResidueModificationMass(String residueModificationMass)
void	setResiduePotentialModificationMass(String residuePotentialModificationMass)
void	setResiduePotentialModificationMotif(String residuePotentialModificationMotif)
void	setScoringAIons(String scoringAIons)
void	setScoringAlgorithm(String scoringAlgorithm)
void	setScoringBIons(String scoringBIons)
void	setScoringCIons(String scoringCIons)
void	setScoringCyclicPermutation(String scoringCyclicPermutation)
void	setScoringIncludeReverse(String scoringIncludeReverse)
void	setScoringMaximumMissedCleavageSites(String scoringMaximumMissedCleavageSites)
void	setScoringMinimumIonCount(String scoringMinimumIonCount)
void	setScoringXIons(String scoringXIons)
void	setScoringYIons(String scoringYIons)
void	setScoringZIons(String scoringZIons)
void	setSpectrumDynamicRange(String spectrumDynamicRange)
void	setSpectrumFragmentMassType(String spectrumFragmentMassType)
void	setSpectrumFragmentMonoisotopicMassError(String spectrumFragmentMonoisotopicMassError)
void	setSpectrumFragmentMonoisotopicMassErrorUnits(String spectrumFragmentMonoisotopicMassErrorUnits)
void	setSpectrumMaximumParentCharge(String spectrumMaximumParentCharge)
void	setSpectrumMaximumParentMPlusH(String spectrumMaximumParentMPlusH)
void	setSpectrumMinimumFragmentMz(String spectrumMinimumFragmentMz)
void	setSpectrumMinimumParentMPlusH(String spectrumMinimumParentMPlusH)
void	setSpectrumMinimumPeaks(String spectrumMinimumPeaks)
void	setSpectrumParentMonoisotopicMassErrorMinus(String spectrumParentMonoisotopicMassErrorMinus)
void	setSpectrumParentMonoisotopicMassErrorPlus(String spectrumParentMonoisotopicMassErrorPlus)
void	setSpectrumParentMonoisotopicMassErrorUnits(String spectrumParentMonoisotopicMassErrorUnits)
void	setSpectrumParentMonoisotopicMassIsotopeError(String spectrumParentMonoisotopicMassIsotopeError)
void	setSpectrumPath(String spectrumPath)
void	setSpectrumSequenceBatchSize(String spectrumSequenceBatchSize)
void	setSpectrumThreads(String spectrumThreads)
void	setSpectrumTotalPeaks(String spectrumTotalPeaks)
void	setSpectrumUseConditioning(String spectrumUseConditioning)
void	setSpectrumUseNoiseSuppression(String spectrumUseNoiseSuppression)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

XTandemParameterSet

public XTandemParameterSet()

Method Detail

getListPathDefaultParameters

public String getListPathDefaultParameters()

Returns:

String list path of default parameters.

setListPathDefaultParameters

public void setListPathDefaultParameters(String listPathDefaultParameters)

Parameters:

listPathDefaultParameters - String list path of default parameters.

getListPathTaxonomyInformation

public String getListPathTaxonomyInformation()

Returns:

String list path of taxonomy information.

setListPathTaxonomyInformation

public void setListPathTaxonomyInformation(String listPathTaxonomyInformation)

Parameters:

listPathTaxonomyInformation - String list path of taxonomy information.

getSpectrumPath

public String getSpectrumPath()

Returns:

String spectrum path.

setSpectrumPath

public void setSpectrumPath(String spectrumPath)

Parameters:

spectrumPath - String spectrum path.

getSpectrumFragmentMonoisotopicMassError

public String getSpectrumFragmentMonoisotopicMassError()

Returns:

String spectrum mass error of monoisotopic fragment.

setSpectrumFragmentMonoisotopicMassError

public void setSpectrumFragmentMonoisotopicMassError(String spectrumFragmentMonoisotopicMassError)

Parameters:

spectrumFragmentMonoisotopicMassError - String spectrum mass error of monoisotopic fragment.

getSpectrumParentMonoisotopicMassErrorPlus

public String getSpectrumParentMonoisotopicMassErrorPlus()

Returns:

String spectrum mass error plus of monoisotopic parent.

setSpectrumParentMonoisotopicMassErrorPlus

public void setSpectrumParentMonoisotopicMassErrorPlus(String spectrumParentMonoisotopicMassErrorPlus)

Parameters:

spectrumParentMonoisotopicMassErrorPlus - String spectrum mass error plus of monoisotopic parent.

getSpectrumParentMonoisotopicMassErrorMinus

public String getSpectrumParentMonoisotopicMassErrorMinus()

Returns:

String spectrum mass error minus of monoisotopic parent.

setSpectrumParentMonoisotopicMassErrorMinus

public void setSpectrumParentMonoisotopicMassErrorMinus(String spectrumParentMonoisotopicMassErrorMinus)

Parameters:

spectrumParentMonoisotopicMassErrorMinus - String spectrum mass error minus of monoisotopic parent.

getSpectrumParentMonoisotopicMassIsotopeError

public String getSpectrumParentMonoisotopicMassIsotopeError()

Returns:

String spectrum mass isotope error of monoisotopic parent.

setSpectrumParentMonoisotopicMassIsotopeError

public void setSpectrumParentMonoisotopicMassIsotopeError(String spectrumParentMonoisotopicMassIsotopeError)

Parameters:

spectrumParentMonoisotopicMassIsotopeError - String spectrum mass isotope error of monoisotopic parent.

getSpectrumFragmentMonoisotopicMassErrorUnits

public String getSpectrumFragmentMonoisotopicMassErrorUnits()

Returns:

String spectrum mass error units of monoisotopic fragment.

setSpectrumFragmentMonoisotopicMassErrorUnits

public void setSpectrumFragmentMonoisotopicMassErrorUnits(String spectrumFragmentMonoisotopicMassErrorUnits)

Parameters:

spectrumFragmentMonoisotopicMassErrorUnits - String spectrum mass error units of monoisotopic fragment.

getSpectrumParentMonoisotopicMassErrorUnits

public String getSpectrumParentMonoisotopicMassErrorUnits()

Returns:

String spectrum mass error units of monoisotopic parent.

setSpectrumParentMonoisotopicMassErrorUnits

public void setSpectrumParentMonoisotopicMassErrorUnits(String spectrumParentMonoisotopicMassErrorUnits)

Parameters:

spectrumParentMonoisotopicMassErrorUnits - String spectrum mass error units of monoisotopic parent.

getSpectrumFragmentMassType

public String getSpectrumFragmentMassType()

Returns:

String spectrum mass type of fragment.

setSpectrumFragmentMassType

public void setSpectrumFragmentMassType(String spectrumFragmentMassType)

Parameters:

spectrumFragmentMassType - String spectrum mass type of fragment.

getSpectrumDynamicRange

public String getSpectrumDynamicRange()

Returns:

String spectrum dynamic range.

setSpectrumDynamicRange

public void setSpectrumDynamicRange(String spectrumDynamicRange)

Parameters:

spectrumDynamicRange - String spectrum dynamic range.

getSpectrumTotalPeaks

public String getSpectrumTotalPeaks()

Returns:

String spectrum total peaks.

setSpectrumTotalPeaks

public void setSpectrumTotalPeaks(String spectrumTotalPeaks)

Parameters:

spectrumTotalPeaks - String spectrum total peaks.

getSpectrumMaximumParentCharge

public String getSpectrumMaximumParentCharge()

Returns:

String spectrum maximum parent charge.

setSpectrumMaximumParentCharge

public void setSpectrumMaximumParentCharge(String spectrumMaximumParentCharge)

Parameters:

spectrumMaximumParentCharge - String spectrum maximum parent charge.

getSpectrumUseNoiseSuppression

public String getSpectrumUseNoiseSuppression()

Returns:

String spectrum use noise suppression.

setSpectrumUseNoiseSuppression

public void setSpectrumUseNoiseSuppression(String spectrumUseNoiseSuppression)

Parameters:

spectrumUseNoiseSuppression - String spectrum use noise suppression.

getSpectrumMinimumParentMPlusH

public String getSpectrumMinimumParentMPlusH()

Returns:

String spectrum minimum parent m+h.

setSpectrumMinimumParentMPlusH

public void setSpectrumMinimumParentMPlusH(String spectrumMinimumParentMPlusH)

Parameters:

spectrumMinimumParentMPlusH - String spectrum minimum parent m+h.

getSpectrumMaximumParentMPlusH

public String getSpectrumMaximumParentMPlusH()

Returns:

String spectrum maximum parent m+h.

setSpectrumMaximumParentMPlusH

public void setSpectrumMaximumParentMPlusH(String spectrumMaximumParentMPlusH)

Parameters:

spectrumMaximumParentMPlusH - String spectrum maximum parent m+h.

getSpectrumMinimumFragmentMz

public String getSpectrumMinimumFragmentMz()

Returns:

String spectrum minimum fragment mz.

setSpectrumMinimumFragmentMz

public void setSpectrumMinimumFragmentMz(String spectrumMinimumFragmentMz)

Parameters:

spectrumMinimumFragmentMz - String spectrum minimum fragment mz.

getSpectrumMinimumPeaks

public String getSpectrumMinimumPeaks()

Returns:

String spectrum minimum peaks.

setSpectrumMinimumPeaks

public void setSpectrumMinimumPeaks(String spectrumMinimumPeaks)

Parameters:

spectrumMinimumPeaks - String spectrum minimum peaks.

getSpectrumThreads

public String getSpectrumThreads()

Returns:

String spectrum threads.

setSpectrumThreads

public void setSpectrumThreads(String spectrumThreads)

Parameters:

spectrumThreads - String spectrum threads.

getSpectrumSequenceBatchSize

public String getSpectrumSequenceBatchSize()

Returns:

String spectrum sequence batch size.

setSpectrumSequenceBatchSize

public void setSpectrumSequenceBatchSize(String spectrumSequenceBatchSize)

Parameters:

spectrumSequenceBatchSize - String spectrum sequence batch size.

getSpectrumUseConditioning

public String getSpectrumUseConditioning()

Returns:

String spectrum use conditioning.

setSpectrumUseConditioning

public void setSpectrumUseConditioning(String spectrumUseConditioning)

Parameters:

spectrumUseConditioning - String spectrum use conditioning.

getResidueModificationMass

public String getResidueModificationMass()

Returns:

String residue modification mass.

setResidueModificationMass

public void setResidueModificationMass(String residueModificationMass)

Parameters:

residueModificationMass - String residue modification mass.

getResiduePotentialModificationMass

public String getResiduePotentialModificationMass()

Returns:

String residue potential modification mass.

setResiduePotentialModificationMass

public void setResiduePotentialModificationMass(String residuePotentialModificationMass)

Parameters:

residuePotentialModificationMass - String residue potential modification mass.

getResiduePotentialModificationMotif

public String getResiduePotentialModificationMotif()

Returns:

String residue potential modification motif.

setResiduePotentialModificationMotif

public void setResiduePotentialModificationMotif(String residuePotentialModificationMotif)

Parameters:

residuePotentialModificationMotif - String residue potential modification motif.

getProteinTaxon

public String getProteinTaxon()

Returns:

String protein taxon.

setProteinTaxon

public void setProteinTaxon(String proteinTaxon)

Parameters:

proteinTaxon - String protein taxon.

getProteinCleavageSite

public String getProteinCleavageSite()

Returns:

String protein cleavage site.

setProteinCleavageSite

public void setProteinCleavageSite(String proteinCleavageSite)

Parameters:

proteinCleavageSite - String protein cleavage site.

getProteinModifiedResidueMassFile

public String getProteinModifiedResidueMassFile()

Returns:

String protein modified residue mass file .

setProteinModifiedResidueMassFile

public void setProteinModifiedResidueMassFile(String proteinModifiedResidueMassFile)

Parameters:

proteinModifiedResidueMassFile - String protein modified residue mass file.

getProteinCleavageNTerminalMassChange

public String getProteinCleavageNTerminalMassChange()

Returns:

String protein cleavage N-terminal mass change.

setProteinCleavageNTerminalMassChange

public void setProteinCleavageNTerminalMassChange(String proteinCleavageNTerminalMassChange)

Parameters:

proteinCleavageNTerminalMassChange - String protein cleavage N-terminal mass change.

getProteinCleavageCTerminalMassChange

public String getProteinCleavageCTerminalMassChange()

Returns:

String protein cleavage C-terminal mass change.

setProteinCleavageCTerminalMassChange

public void setProteinCleavageCTerminalMassChange(String proteinCleavageCTerminalMassChange)

Parameters:

proteinCleavageCTerminalMassChange - String protein cleavage C-terminal mass change.

getProteinNTerminalResidueModificationMass

public String getProteinNTerminalResidueModificationMass()

Returns:

String protein N-terminal residue modification mass.

setProteinNTerminalResidueModificationMass

public void setProteinNTerminalResidueModificationMass(String proteinNTerminalResidueModificationMass)

Parameters:

proteinNTerminalResidueModificationMass - String protein N-terminal residue modification mass.

getProteinCTerminalResidueModificationMass

public String getProteinCTerminalResidueModificationMass()

Returns:

String protein C-terminal residue modification mass.

setProteinCTerminalResidueModificationMass

public void setProteinCTerminalResidueModificationMass(String proteinCTerminalResidueModificationMass)

Parameters:

proteinCTerminalResidueModificationMass - String protein C-terminal residue modification mass.

getProteinHomologManagement

public String getProteinHomologManagement()

Returns:

String protein homolog management.

setProteinHomologManagement

public void setProteinHomologManagement(String proteinHomologManagement)

Parameters:

proteinHomologManagement - String protein homolog management.

getRefine

public String getRefine()

Returns:

String refine.

setRefine

public void setRefine(String refine)

Parameters:

refine - String refine.

getRefineModificationMass

public String getRefineModificationMass()

Returns:

String refine modification mass.

setRefineModificationMass

public void setRefineModificationMass(String refineModificationMass)

Parameters:

refineModificationMass - String refine modification mass.

getRefineSequencePath

public String getRefineSequencePath()

Returns:

String refine sequence path.

setRefineSequencePath

public void setRefineSequencePath(String refineSequencePath)

Parameters:

refineSequencePath - String refine sequence path.

getRefineTicPercent

public String getRefineTicPercent()

Returns:

String refine tic percent.

setRefineTicPercent

public void setRefineTicPercent(String refineTicPercent)

Parameters:

refineTicPercent - String refine tic percent.

getRefineSpectrumSynthesis

public String getRefineSpectrumSynthesis()

Returns:

String refine spectrum synthesis.

setRefineSpectrumSynthesis

public void setRefineSpectrumSynthesis(String refineSpectrumSynthesis)

Parameters:

refineSpectrumSynthesis - String refine spectrum synthesis.

getRefineMaximumValidExpectationValue

public String getRefineMaximumValidExpectationValue()

Returns:

String refine maximum valid expectation value.

setRefineMaximumValidExpectationValue

public void setRefineMaximumValidExpectationValue(String refineMaximumValidExpectationValue)

Parameters:

refineMaximumValidExpectationValue - String refine maximum valid expectation value.

getRefinePotentialNTerminusModifications

public String getRefinePotentialNTerminusModifications()

Returns:

String refine potential N-terminus modifications.

setRefinePotentialNTerminusModifications

public void setRefinePotentialNTerminusModifications(String refinePotentialNTerminusModifications)

Parameters:

refinePotentialNTerminusModifications - String refine potential N-terminus modifications.

getRefinePotentialCTerminusModifications

public String getRefinePotentialCTerminusModifications()

Returns:

String refine potential C-terminus modifications.

setRefinePotentialCTerminusModifications

public void setRefinePotentialCTerminusModifications(String refinePotentialCTerminusModifications)

Parameters:

refinePotentialCTerminusModifications - String refine potential C-terminus modifications.

getRefineUnanticipatedCleavage

public String getRefineUnanticipatedCleavage()

Returns:

String refine unanticipated cleavage.

setRefineUnanticipatedCleavage

public void setRefineUnanticipatedCleavage(String refineUnanticipatedCleavage)

Parameters:

refineUnanticipatedCleavage - String refine unanticipated cleavage.

getRefinePotentialModificationMass

public String getRefinePotentialModificationMass()

Returns:

String refine potential modification mass.

setRefinePotentialModificationMass

public void setRefinePotentialModificationMass(String refinePotentialModificationMass)

Parameters:

refinePotentialModificationMass - String refine potential modification mass.

getRefinePointMutations

public String getRefinePointMutations()

Returns:

String refine point mutations.

setRefinePointMutations

public void setRefinePointMutations(String refinePointMutations)

Parameters:

refinePointMutations - String refine point mutations.

getRefineUsePotentialModificationsForFullRefinement

public String getRefineUsePotentialModificationsForFullRefinement()

Returns:

String refine use potential modifications for full refinement.

setRefineUsePotentialModificationsForFullRefinement

public void setRefineUsePotentialModificationsForFullRefinement(String refineUsePotentialModificationsForFullRefinement)

Parameters:

refineUsePotentialModificationsForFullRefinement - String refine use potential modifications for full refinement.

getRefinePotentialModificationMotif

public String getRefinePotentialModificationMotif()

Returns:

String refine point modification motif.

setRefinePotentialModificationMotif

public void setRefinePotentialModificationMotif(String refinePotentialModificationMotif)

Parameters:

refinePotentialModificationMotif - String refine point modification motif.

getScoringMinimumIonCount

public String getScoringMinimumIonCount()

Returns:

String scoring minimum ion count.

setScoringMinimumIonCount

public void setScoringMinimumIonCount(String scoringMinimumIonCount)

Parameters:

scoringMinimumIonCount - String scoring minimum ion count.

getScoringMaximumMissedCleavageSites

public String getScoringMaximumMissedCleavageSites()

Returns:

String scoring maximum missed cleavage sites.

setScoringMaximumMissedCleavageSites

public void setScoringMaximumMissedCleavageSites(String scoringMaximumMissedCleavageSites)

Parameters:

scoringMaximumMissedCleavageSites - String scoring maximum missed cleavage sites.

getScoringXIons

public String getScoringXIons()

Returns:

String scoring x ions.

setScoringXIons

public void setScoringXIons(String scoringXIons)

Parameters:

scoringXIons - String scoring x ions.

getScoringYIons

public String getScoringYIons()

Returns:

String scoring y ions.

setScoringYIons

public void setScoringYIons(String scoringYIons)

Parameters:

scoringYIons - String scoring y ions.

getScoringZIons

public String getScoringZIons()

Returns:

String scoring z ions.

setScoringZIons

public void setScoringZIons(String scoringZIons)

Parameters:

scoringZIons - String scoring z ions.

getScoringAIons

public String getScoringAIons()

Returns:

String scoring a ions.

setScoringAIons

public void setScoringAIons(String scoringAIons)

Parameters:

scoringAIons - String scoring a ions.

getScoringBIons

public String getScoringBIons()

Returns:

String scoring b ions.

setScoringBIons

public void setScoringBIons(String scoringBIons)

Parameters:

scoringBIons - String scoring b ions.

getScoringCIons

public String getScoringCIons()

Returns:

String scoring c ions.

setScoringCIons

public void setScoringCIons(String scoringCIons)

Parameters:

scoringCIons - String scoring c ions.

getScoringCyclicPermutation

public String getScoringCyclicPermutation()

Returns:

String scoring cyclic permutation.

setScoringCyclicPermutation

public void setScoringCyclicPermutation(String scoringCyclicPermutation)

Parameters:

scoringCyclicPermutation - String scoring cyclic permutation.

getScoringIncludeReverse

public String getScoringIncludeReverse()

Returns:

String scoring include reverse.

setScoringIncludeReverse

public void setScoringIncludeReverse(String scoringIncludeReverse)

Parameters:

scoringIncludeReverse - String scoring include reverse.

getScoringAlgorithm

public String getScoringAlgorithm()

Returns:

String scoring algorithm.

setScoringAlgorithm

public void setScoringAlgorithm(String scoringAlgorithm)

Parameters:

scoringAlgorithm - String scoring algorithm.

getOutputPath

public String getOutputPath()

Returns:

String output path.

setOutputPath

public void setOutputPath(String outputPath)

Parameters:

outputPath - String output path.

getOutputLogPath

public String getOutputLogPath()

Returns:

String output log path.

setOutputLogPath

public void setOutputLogPath(String outputLogPath)

Parameters:

outputLogPath - String output log path.

getOutputMessage

public String getOutputMessage()

Returns:

String output message.

setOutputMessage

public void setOutputMessage(String outputMessage)

Parameters:

outputMessage - String output message.

getOutputSequencePath

public String getOutputSequencePath()

Returns:

String output sequence path.

setOutputSequencePath

public void setOutputSequencePath(String outputSequencePath)

Parameters:

outputSequencePath - String output sequence path.

getOutputSortResultsBy

public String getOutputSortResultsBy()

Returns:

String output sort results by.

setOutputSortResultsBy

public void setOutputSortResultsBy(String outputSortResultsBy)

Parameters:

outputSortResultsBy - String output sort results by.

getOutputPathHashing

public String getOutputPathHashing()

Returns:

String output path hashing.

setOutputPathHashing

public void setOutputPathHashing(String outputPathHashing)

Parameters:

outputPathHashing - String output path hashing.

getOutputXslPath

public String getOutputXslPath()

Returns:

String output xsl path.

setOutputXslPath

public void setOutputXslPath(String outputXslPath)

Parameters:

outputXslPath - String output xsl path.

getOutputParameters

public String getOutputParameters()

Returns:

String output parameters.

setOutputParameters

public void setOutputParameters(String outputParameters)

Parameters:

outputParameters - String output parameters.

getOutputPerformance

public String getOutputPerformance()

Returns:

String output performance.

setOutputPerformance

public void setOutputPerformance(String outputPerformance)

Parameters:

outputPerformance - String output performance.

getOutputSpectra

public String getOutputSpectra()

Returns:

String output spectra.

setOutputSpectra

public void setOutputSpectra(String outputSpectra)

Parameters:

outputSpectra - String output spectra.

getOutputHistograms

public String getOutputHistograms()

Returns:

String output histograms.

setOutputHistograms

public void setOutputHistograms(String outputHistograms)

Parameters:

outputHistograms - String output histograms.

getOutputProteins

public String getOutputProteins()

Returns:

String output proteins.

setOutputProteins

public void setOutputProteins(String outputProteins)

Parameters:

outputProteins - String output proteins.

getOutputSequences

public String getOutputSequences()

Returns:

String output sequences.

setOutputSequences

public void setOutputSequences(String outputSequences)

Parameters:

outputSequences - String output sequences.

getOutputOneSequenceCopy

public String getOutputOneSequenceCopy()

Returns:

String output one sequence copy.

setOutputOneSequenceCopy

public void setOutputOneSequenceCopy(String outputOneSequenceCopy)

Parameters:

outputOneSequenceCopy - String output one sequence copy.

getOutputResults

public String getOutputResults()

Returns:

String output results.

setOutputResults

public void setOutputResults(String outputResults)

Parameters:

outputResults - String output results.

getOutputMaximumValidExpectationValue

public String getOutputMaximumValidExpectationValue()

Returns:

String output maximum valid expectation value.

setOutputMaximumValidExpectationValue

public void setOutputMaximumValidExpectationValue(String outputMaximumValidExpectationValue)

Parameters:

outputMaximumValidExpectationValue - String output maximum valid expectation value.

getOutputHistogramColumnWidth

public String getOutputHistogramColumnWidth()

Returns:

outputHistogramColumnWidth String output histogram column width.

setOutputHistogramColumnWidth

public void setOutputHistogramColumnWidth(String outputHistogramColumnWidth)

Parameters:

outputHistogramColumnWidth - String output histogram column width.