public class OmssaParameters extends Object implements IdentificationAlgorithmParameter
Constructor and Description |
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OmssaParameters()
Constructor.
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Modifier and Type | Method and Description |
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boolean |
equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
Indicates whether another identificationAlgorithmParameter has the same
parameters.
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Advocate |
getAlgorithm()
Returns the identification algorithm.
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Double |
getConsecutiveIonProbability()
Returns the consecutive ion probability.
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Integer |
getDoubleChargeWindow()
Returns the window size for doubly charged ions.
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Double |
getFractionOfPeaksForChargeEstimation()
Returns the fraction of peaks to be retained for charge >1 estimation.
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Double |
getHighIntensityCutOff()
Returns the high intensity cut-off as percentage of the most intense ion
peak.
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Integer |
getHitListLength()
Returns the length of the hit list for OMSSA.
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Double |
getIntensityCutOffIncrement()
Returns the intensity cut-off increment.
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Double |
getIterativeReplaceEvalue()
Returns the e-value threshold to use to replace a hit for the iterative
search.
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Double |
getIterativeSequenceEvalue()
Returns the e-value threshold to use to consider a sequence for the
iterative search.
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Double |
getIterativeSpectrumEvalue()
Returns the e-value threshold to use consider a spectrum for the
iterative search.
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Double |
getLowIntensityCutOff()
Returns the low intensity cut-off as percentage of the most intense ion
peak.
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Double |
getMaxEValue()
Returns the maximal e-value searched for.
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Integer |
getMaxFragmentCharge()
Returns the maximal fragment charge.
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Integer |
getMaxFragmentPerSeries()
Returns the maximal number of fragments to retain per series.
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Integer |
getMaxHitsPerSpectrumPerCharge()
Returns the maximal number of hits searched per spectrum and per charge.
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Integer |
getMaxMzLadders()
Returns the maximal m/z ladder length.
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Integer |
getMaxPeptideLength()
Returns the maximal peptide length allowed.
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Integer |
getMinAnnotatedPeaks()
Returns the minimal number of annotated peaks a peptide should have.
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Charge |
getMinimalChargeForMultipleChargedFragments()
Returns the minimal precursor charge to account for multiply charged
fragments in OMSSA.
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Integer |
getMinPeaks()
Returns the minimal number of peaks a spectrum should contain.
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Integer |
getMinPeptideLength()
Sets the minimal peptide length allowed.
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Integer |
getMinPrecPerSpectrum()
Returns the minimal number of precursors per spectrum.
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Integer |
getnAnnotatedMostIntensePeaks()
Returns the minimal number of annotated most intense peaks.
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Double |
getNeutronThreshold()
Returns the mass after which exact neutron mass should be considered in
the calculation.
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ArrayList<Integer> |
getNoProlineRuleSeries()
Returns the id numbers of ion series to apply no product ions at proline
rule at.
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Integer |
getnPeaksInDoubleChargeWindow()
Returns the number of peaks in doubly charged windows.
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Integer |
getnPeaksInSingleChargeWindow()
Returns the number of peaks in singly charged windows.
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Integer |
getNumberOfItotopicPeaks()
Returns the number of isotopic peaks to consider.
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static String[] |
getOmssaOutputTypes()
Returns the output types available.
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String |
getSelectedOutput()
Returns the selected output type, omx or csv.
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Integer |
getSingleChargeWindow()
Returns the window size for singly charged ions.
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Boolean |
isCleaveNterMethionine()
Indicates whether N-terminal methionines should be cleaved.
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Boolean |
isDetermineChargePlusOneAlgorithmically()
Indicates whether charge plus one should be determined algorithmically.
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Boolean |
isEstimateCharge()
Indicates whether the precursor charge shall be estimated for OMSSA.
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Boolean |
isMemoryMappedSequenceLibraries()
Indicates whether sequence libraries should be mapped in memory.
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Boolean |
isRemovePrecursor()
Indicates whether the precursor shall be removed for OMSSA.
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Boolean |
isScalePrecursor()
Indicates whether the precursor shall be scaled for OMSSA.
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Boolean |
isSearchForwardFragmentFirst()
Indicates whether forward ions (b1) should be searched first.
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Boolean |
isSearchPositiveIons()
Indicates whether positive ions are searched.
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Boolean |
isSearchRewindFragments()
Indicates whether C-terminal fragments should be searched.
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Boolean |
isUseCorrelationCorrectionScore()
Indicates whether the correlation correction score should be used.
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void |
setCleaveNterMethionine(Boolean cleaveNterMethionine)
Sets whether N-terminal methionines should be cleaved.
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void |
setConsecutiveIonProbability(Double consecutiveIonProbability)
Set the consecutive ion probability.
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void |
setDetermineChargePlusOneAlgorithmically(Boolean determineChargePlusOneAlgorithmically)
Sets whether charge plus one should be determined algorithmically.
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void |
setDoubleChargeWindow(Integer doubleChargeWindow)
Sets the window size for doubly charged ions.
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void |
setEstimateCharge(Boolean estimateCharge)
Sets whether the precursor charge shall be estimated for OMSSA.
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void |
setFractionOfPeaksForChargeEstimation(Double fractionOfPeaksForChargeEstimation)
Sets the fraction of peaks to be retained for charge >1 estimation.
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void |
setHighIntensityCutOff(Double highIntensityCutOff)
Sets the high intensity cut-off as percentage of the most intense ion
peak.
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void |
setHitListLength(Integer hitListLength)
Sets the length of the hit list for OMSSA.
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void |
setIntensityCutOffIncrement(Double intensityCutOffIncrement)
Sets the intensity cut-off increment.
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void |
setIterativeReplaceEvalue(Double iterativeReplaceEvalue)
Sets the e-value threshold to use to replace a hit for the iterative
search.
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void |
setIterativeSequenceEvalue(Double iterativeSequenceEvalue)
Sets the e-value threshold to use to consider a sequence for the
iterative search.
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void |
setIterativeSpectrumEvalue(Double iterativeSpectrumEvalue)
Sets the e-value threshold to use consider a spectrum for the iterative
search.
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void |
setLowIntensityCutOff(Double lowIntensityCutOff)
Sets the low intensity cut-off as percentage of the most intense ion
peak.
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void |
setMaxEValue(Double maxEValue)
Sets the maximal e-value searched for.
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void |
setMaxFragmentCharge(Integer maxFragmentCharge)
Sets the maximal fragment charge.
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void |
setMaxFragmentPerSeries(Integer maxFragmentPerSeries)
Sets the maximal number of fragments to retain per series.
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void |
setMaxHitsPerSpectrumPerCharge(Integer maxHitsPerSpectrumPerCharge)
Set the maximal number of hits searched per spectrum and per charge.
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void |
setMaxMzLadders(Integer maxMzLadders)
Sets the maximal m/z ladder length.
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void |
setMaxPeptideLength(Integer maxPeptideLength)
Sets the maximal peptide length allowed.
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void |
setMemoryMappedSequenceLibraries(Boolean memoryMappedSequenceLibraries)
Sets whether sequence libraries should be mapped in memory.
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void |
setMinAnnotatedPeaks(Integer minAnnotatedPeaks)
Sets the minimal number of annotated peaks a peptide should have.
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void |
setMinimalChargeForMultipleChargedFragments(Charge minimalChargeForMultipleChargedFragments)
Sets the minimal precursor charge to account for multiply charged
fragments in OMSSA.
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void |
setMinPeaks(Integer minPeaks)
Sets the minimal number of peaks a spectrum should contain.
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void |
setMinPeptideLength(Integer minPeptideLength)
Sets the minimal peptide length allowed.
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void |
setMinPrecPerSpectrum(Integer minPrecPerSpectrum)
Sets the minimal number of precursors per spectrum.
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void |
setnAnnotatedMostIntensePeaks(Integer nAnnotatedMostIntensePeaks)
Sets the minimal number of annotated most intense peaks.
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void |
setNeutronThreshold(Double neutronThreshold)
Sets the mass after which exact neutron mass should be considered in the
calculation.
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void |
setNoProlineRuleSeries(ArrayList<Integer> noProlineRuleSeries)
Sets the id numbers of ion series to apply no product ions at proline
rule at.
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void |
setnPeaksInDoubleChargeWindow(Integer nPeaksInDoubleChargeWindow)
Sets the number of peaks in doubly charged windows.
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void |
setnPeaksInSingleChargeWindow(Integer nPeaksInSingleChargeWindow)
Sets the number of peaks in singly charged windows.
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void |
setNumberOfItotopicPeaks(Integer numberOfItotopicPeaks)
Sets the number of isotopic peaks to consider.
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void |
setRemovePrecursor(Boolean removePrecursor)
Sets whether the precursor shall be removed for OMSSA.
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void |
setScalePrecursor(Boolean scalePrecursor)
Sets whether the precursor shall be scaled for OMSSA.
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void |
setSearchForwardFragmentFirst(Boolean searchForwardFragmentFirst)
Sets whether forward ions (b1) should be searched first.
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void |
setSearchPositiveIons(Boolean searchPositiveIons)
Sets whether positive ions are searched.
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void |
setSearchRewindFragments(Boolean searchRewindFragments)
Sets whether C-terminal fragments should be searched.
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void |
setSelectedOutput(String selectedOutput)
Sets the output type, omx or csv.
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void |
setSingleChargeWindow(Integer singleChargeWindow)
Sets the window size for singly charged ions.
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void |
setUseCorrelationCorrectionScore(Boolean useCorrelationCorrectionScore)
Sets whether the correlation correction score should be used.
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String |
toString(boolean html)
Returns the parameters as a string.
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public Double getMaxEValue()
public void setMaxEValue(Double maxEValue)
maxEValue
- the maximal e-value searched forpublic Integer getHitListLength()
public void setHitListLength(Integer hitListLength)
hitListLength
- the length of the hit list for OMSSApublic Charge getMinimalChargeForMultipleChargedFragments()
public void setMinimalChargeForMultipleChargedFragments(Charge minimalChargeForMultipleChargedFragments)
minimalChargeForMultipleChargedFragments
- the minimal precursor
charge to account for multiply charged fragments in OMSSApublic Integer getMaxPeptideLength()
public void setMaxPeptideLength(Integer maxPeptideLength)
maxPeptideLength
- the maximal peptide length allowedpublic Integer getMinPeptideLength()
public void setMinPeptideLength(Integer minPeptideLength)
minPeptideLength
- the minimal peptide length allowedpublic Boolean isEstimateCharge()
public void setEstimateCharge(Boolean estimateCharge)
estimateCharge
- a boolean indicating whether the precursor charge
shall be estimated for OMSSApublic Boolean isRemovePrecursor()
public void setRemovePrecursor(Boolean removePrecursor)
removePrecursor
- a boolean indicating whether the precursor shall
be removed for OMSSApublic Boolean isScalePrecursor()
public void setScalePrecursor(Boolean scalePrecursor)
scalePrecursor
- a boolean indicating whether the precursor shall be
scaled for OMSSApublic String getSelectedOutput()
public void setSelectedOutput(String selectedOutput)
selectedOutput
- the output typepublic static String[] getOmssaOutputTypes()
public Boolean isMemoryMappedSequenceLibraries()
public void setMemoryMappedSequenceLibraries(Boolean memoryMappedSequenceLibraries)
memoryMappedSequenceLibraries
- a boolean indicating whether
sequence libraries should be mapped in memorypublic Integer getNumberOfItotopicPeaks()
public void setNumberOfItotopicPeaks(Integer numberOfItotopicPeaks)
numberOfItotopicPeaks
- the number of isotopic peaks to considerpublic Double getNeutronThreshold()
public void setNeutronThreshold(Double neutronThreshold)
neutronThreshold
- the mass after which exact neutron mass should be
considered in the calculationpublic Double getLowIntensityCutOff()
public void setLowIntensityCutOff(Double lowIntensityCutOff)
lowIntensityCutOff
- the low intensity cut-off as percentage of the
most intense ion peakpublic Double getHighIntensityCutOff()
public void setHighIntensityCutOff(Double highIntensityCutOff)
highIntensityCutOff
- the high intensity cut-off as percentage of
the most intense ion peakpublic Double getIntensityCutOffIncrement()
public void setIntensityCutOffIncrement(Double intensityCutOffIncrement)
intensityCutOffIncrement
- the intensity cut-off incrementpublic Integer getSingleChargeWindow()
public void setSingleChargeWindow(Integer singleChargeWindow)
singleChargeWindow
- the window size for singly charged ionspublic Integer getDoubleChargeWindow()
public void setDoubleChargeWindow(Integer doubleChargeWindow)
doubleChargeWindow
- the window size for doubly charged ionspublic Integer getnPeaksInSingleChargeWindow()
public void setnPeaksInSingleChargeWindow(Integer nPeaksInSingleChargeWindow)
nPeaksInSingleChargeWindow
- the number of peaks in singly charged
windowspublic Integer getnPeaksInDoubleChargeWindow()
public void setnPeaksInDoubleChargeWindow(Integer nPeaksInDoubleChargeWindow)
nPeaksInDoubleChargeWindow
- the number of peaks in doubly charged
windowspublic Integer getMaxHitsPerSpectrumPerCharge()
public void setMaxHitsPerSpectrumPerCharge(Integer maxHitsPerSpectrumPerCharge)
maxHitsPerSpectrumPerCharge
- the maximal number of hits searched
per spectrum and per chargepublic Integer getnAnnotatedMostIntensePeaks()
public void setnAnnotatedMostIntensePeaks(Integer nAnnotatedMostIntensePeaks)
nAnnotatedMostIntensePeaks
- the minimal number of annotated most
intense peakspublic Integer getMinAnnotatedPeaks()
public void setMinAnnotatedPeaks(Integer minAnnotatedPeaks)
minAnnotatedPeaks
- the minimal number of annotated peaks a peptide
should havepublic Integer getMinPeaks()
public void setMinPeaks(Integer minPeaks)
minPeaks
- the minimal number of peaks a spectrum should containpublic Boolean isCleaveNterMethionine()
public void setCleaveNterMethionine(Boolean cleaveNterMethionine)
cleaveNterMethionine
- whether N-terminal methionines should be
cleavedpublic Integer getMaxMzLadders()
public void setMaxMzLadders(Integer maxMzLadders)
maxMzLadders
- the maximal m/z ladder lengthpublic Integer getMaxFragmentCharge()
public void setMaxFragmentCharge(Integer maxFragmentCharge)
maxFragmentCharge
- the maximal fragment chargepublic Double getFractionOfPeaksForChargeEstimation()
public void setFractionOfPeaksForChargeEstimation(Double fractionOfPeaksForChargeEstimation)
fractionOfPeaksForChargeEstimation
- the fraction of peaks to be
retained for charge >1 estimationpublic Boolean isDetermineChargePlusOneAlgorithmically()
public void setDetermineChargePlusOneAlgorithmically(Boolean determineChargePlusOneAlgorithmically)
determineChargePlusOneAlgorithmically
- whether charge plus one
should be determined algorithmicallypublic Boolean isSearchPositiveIons()
public void setSearchPositiveIons(Boolean searchPositiveIons)
searchPositiveIons
- a boolean indicating whether positive ions are
searchedpublic Integer getMinPrecPerSpectrum()
public void setMinPrecPerSpectrum(Integer minPrecPerSpectrum)
minPrecPerSpectrum
- the minimal number of precursors per spectrumpublic Boolean isSearchForwardFragmentFirst()
public void setSearchForwardFragmentFirst(Boolean searchForwardFragmentFirst)
searchForwardFragmentFirst
- whether forward ions (b1) should be
searched firstpublic Boolean isSearchRewindFragments()
public void setSearchRewindFragments(Boolean searchRewindFragments)
searchRewindFragments
- whether C-terminal fragments should be
searchedpublic Integer getMaxFragmentPerSeries()
public void setMaxFragmentPerSeries(Integer maxFragmentPerSeries)
maxFragmentPerSeries
- the maximal number of fragments to retain per
seriespublic Boolean isUseCorrelationCorrectionScore()
public void setUseCorrelationCorrectionScore(Boolean useCorrelationCorrectionScore)
useCorrelationCorrectionScore
- a boolean indicating whether the
correlation correction score should be usedpublic Double getConsecutiveIonProbability()
public void setConsecutiveIonProbability(Double consecutiveIonProbability)
consecutiveIonProbability
- the consecutive ion probabilitypublic Double getIterativeSequenceEvalue()
public void setIterativeSequenceEvalue(Double iterativeSequenceEvalue)
iterativeSequenceEvalue
- the e-value threshold to use to consider a
sequence for the iterative searchpublic Double getIterativeReplaceEvalue()
public void setIterativeReplaceEvalue(Double iterativeReplaceEvalue)
iterativeReplaceEvalue
- the e-value threshold to use to replace a
hit for the iterative searchpublic Double getIterativeSpectrumEvalue()
public void setIterativeSpectrumEvalue(Double iterativeSpectrumEvalue)
iterativeSpectrumEvalue
- the e-value threshold to use consider a
spectrum for the iterative searchpublic ArrayList<Integer> getNoProlineRuleSeries()
public void setNoProlineRuleSeries(ArrayList<Integer> noProlineRuleSeries)
noProlineRuleSeries
- the id numbers of ion series to apply no
product ions at proline rule atpublic Advocate getAlgorithm()
IdentificationAlgorithmParameter
getAlgorithm
in interface IdentificationAlgorithmParameter
public boolean equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
IdentificationAlgorithmParameter
equals
in interface IdentificationAlgorithmParameter
identificationAlgorithmParameter
- the other
identificationAlgorithmParameterpublic String toString(boolean html)
IdentificationAlgorithmParameter
toString
in interface IdentificationAlgorithmParameter
html
- use HTML formattingCopyright © 2015. All rights reserved.