OmssaParameters (computational omics utilities 4.5.7 API)

java.lang.Object
- com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters

All Implemented Interfaces:

IdentificationAlgorithmParameter, Serializable
```
public class OmssaParameters
extends Object
implements IdentificationAlgorithmParameter
```
The OMSSA specific parameters.

Author:

Marc Vaudel

See Also:

Serialized Form

Constructor Summary

Constructors
Constructor and Description

OmssaParameters()
Constructor.

Constructors
Constructor and Description
`OmssaParameters()` Constructor.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)` Indicates whether another identificationAlgorithmParameter has the same parameters.
`Advocate`	`getAlgorithm()` Returns the identification algorithm.
`Double`	`getConsecutiveIonProbability()` Returns the consecutive ion probability.
`Integer`	`getDoubleChargeWindow()` Returns the window size for doubly charged ions.
`Double`	`getFractionOfPeaksForChargeEstimation()` Returns the fraction of peaks to be retained for charge >1 estimation.
`Double`	`getHighIntensityCutOff()` Returns the high intensity cut-off as percentage of the most intense ion peak.
`Integer`	`getHitListLength()` Returns the length of the hit list for OMSSA.
`Double`	`getIntensityCutOffIncrement()` Returns the intensity cut-off increment.
`Double`	`getIterativeReplaceEvalue()` Returns the e-value threshold to use to replace a hit for the iterative search.
`Double`	`getIterativeSequenceEvalue()` Returns the e-value threshold to use to consider a sequence for the iterative search.
`Double`	`getIterativeSpectrumEvalue()` Returns the e-value threshold to use consider a spectrum for the iterative search.
`Double`	`getLowIntensityCutOff()` Returns the low intensity cut-off as percentage of the most intense ion peak.
`Double`	`getMaxEValue()` Returns the maximal e-value searched for.
`Integer`	`getMaxFragmentCharge()` Returns the maximal fragment charge.
`Integer`	`getMaxFragmentPerSeries()` Returns the maximal number of fragments to retain per series.
`Integer`	`getMaxHitsPerSpectrumPerCharge()` Returns the maximal number of hits searched per spectrum and per charge.
`Integer`	`getMaxMzLadders()` Returns the maximal m/z ladder length.
`Integer`	`getMaxPeptideLength()` Returns the maximal peptide length allowed.
`Integer`	`getMinAnnotatedPeaks()` Returns the minimal number of annotated peaks a peptide should have.
`Charge`	`getMinimalChargeForMultipleChargedFragments()` Returns the minimal precursor charge to account for multiply charged fragments in OMSSA.
`Integer`	`getMinPeaks()` Returns the minimal number of peaks a spectrum should contain.
`Integer`	`getMinPeptideLength()` Sets the minimal peptide length allowed.
`Integer`	`getMinPrecPerSpectrum()` Returns the minimal number of precursors per spectrum.
`String`	`getModificationName(int ptmIndex)` Returns the name of the modification indexed by the given index.
`Integer`	`getnAnnotatedMostIntensePeaks()` Returns the minimal number of annotated most intense peaks.
`Double`	`getNeutronThreshold()` Returns the mass after which exact neutron mass should be considered in the calculation.
`ArrayList<Integer>`	`getNoProlineRuleSeries()` Returns the id numbers of ion series to apply no product ions at proline rule at.
`Integer`	`getnPeaksInDoubleChargeWindow()` Returns the number of peaks in doubly charged windows.
`Integer`	`getnPeaksInSingleChargeWindow()` Returns the number of peaks in singly charged windows.
`static HashMap<String,Integer>`	`getOMSSAIndexes(File modificationsFile)` Imports the OMSSA indexes from an XML file.
`static String[]`	`getOmssaOutputTypes()` Returns the output types available.
`Integer`	`getPtmIndex(String modificationName)` Returns the index of a given modification, null if not found.
`HashMap<Integer,String>`	`getPtmIndexes()` Returns the PTM indexes as a map.
`String`	`getSelectedOutput()` Returns the selected output type, omx, csv or pepXML.
`Integer`	`getSingleChargeWindow()` Returns the window size for singly charged ions.
`boolean`	`hasPtmIndexes()` Indicates whether the modification profile has PTM indexes.
`Boolean`	`isCleaveNterMethionine()` Indicates whether N-terminal methionines should be cleaved.
`Boolean`	`isDetermineChargePlusOneAlgorithmically()` Indicates whether charge plus one should be determined algorithmically.
`Boolean`	`isEstimateCharge()` Indicates whether the precursor charge shall be estimated for OMSSA.
`Boolean`	`isMemoryMappedSequenceLibraries()` Indicates whether sequence libraries should be mapped in memory.
`Boolean`	`isRemovePrecursor()` Indicates whether the precursor shall be removed for OMSSA.
`Boolean`	`isScalePrecursor()` Indicates whether the precursor shall be scaled for OMSSA.
`Boolean`	`isSearchForwardFragmentFirst()` Indicates whether forward ions (b1) should be searched first.
`Boolean`	`isSearchPositiveIons()` Indicates whether positive ions are searched.
`Boolean`	`isSearchRewindFragments()` Indicates whether C-terminal fragments should be searched.
`Boolean`	`isUseCorrelationCorrectionScore()` Indicates whether the correlation correction score should be used.
`void`	`setCleaveNterMethionine(Boolean cleaveNterMethionine)` Sets whether N-terminal methionines should be cleaved.
`void`	`setConsecutiveIonProbability(Double consecutiveIonProbability)` Set the consecutive ion probability.
`void`	`setDetermineChargePlusOneAlgorithmically(Boolean determineChargePlusOneAlgorithmically)` Sets whether charge plus one should be determined algorithmically.
`void`	`setDoubleChargeWindow(Integer doubleChargeWindow)` Sets the window size for doubly charged ions.
`void`	`setEstimateCharge(Boolean estimateCharge)` Sets whether the precursor charge shall be estimated for OMSSA.
`void`	`setFractionOfPeaksForChargeEstimation(Double fractionOfPeaksForChargeEstimation)` Sets the fraction of peaks to be retained for charge >1 estimation.
`void`	`setHighIntensityCutOff(Double highIntensityCutOff)` Sets the high intensity cut-off as percentage of the most intense ion peak.
`void`	`setHitListLength(Integer hitListLength)` Sets the length of the hit list for OMSSA.
`void`	`setIntensityCutOffIncrement(Double intensityCutOffIncrement)` Sets the intensity cut-off increment.
`void`	`setIterativeReplaceEvalue(Double iterativeReplaceEvalue)` Sets the e-value threshold to use to replace a hit for the iterative search.
`void`	`setIterativeSequenceEvalue(Double iterativeSequenceEvalue)` Sets the e-value threshold to use to consider a sequence for the iterative search.
`void`	`setIterativeSpectrumEvalue(Double iterativeSpectrumEvalue)` Sets the e-value threshold to use consider a spectrum for the iterative search.
`void`	`setLowIntensityCutOff(Double lowIntensityCutOff)` Sets the low intensity cut-off as percentage of the most intense ion peak.
`void`	`setMaxEValue(Double maxEValue)` Sets the maximal e-value searched for.
`void`	`setMaxFragmentCharge(Integer maxFragmentCharge)` Sets the maximal fragment charge.
`void`	`setMaxFragmentPerSeries(Integer maxFragmentPerSeries)` Sets the maximal number of fragments to retain per series.
`void`	`setMaxHitsPerSpectrumPerCharge(Integer maxHitsPerSpectrumPerCharge)` Set the maximal number of hits searched per spectrum and per charge.
`void`	`setMaxMzLadders(Integer maxMzLadders)` Sets the maximal m/z ladder length.
`void`	`setMaxPeptideLength(Integer maxPeptideLength)` Sets the maximal peptide length allowed.
`void`	`setMemoryMappedSequenceLibraries(Boolean memoryMappedSequenceLibraries)` Sets whether sequence libraries should be mapped in memory.
`void`	`setMinAnnotatedPeaks(Integer minAnnotatedPeaks)` Sets the minimal number of annotated peaks a peptide should have.
`void`	`setMinimalChargeForMultipleChargedFragments(Charge minimalChargeForMultipleChargedFragments)` Sets the minimal precursor charge to account for multiply charged fragments in OMSSA.
`void`	`setMinPeaks(Integer minPeaks)` Sets the minimal number of peaks a spectrum should contain.
`void`	`setMinPeptideLength(Integer minPeptideLength)` Sets the minimal peptide length allowed.
`void`	`setMinPrecPerSpectrum(Integer minPrecPerSpectrum)` Sets the minimal number of precursors per spectrum.
`void`	`setnAnnotatedMostIntensePeaks(Integer nAnnotatedMostIntensePeaks)` Sets the minimal number of annotated most intense peaks.
`void`	`setNeutronThreshold(Double neutronThreshold)` Sets the mass after which exact neutron mass should be considered in the calculation.
`void`	`setNoProlineRuleSeries(ArrayList<Integer> noProlineRuleSeries)` Sets the id numbers of ion series to apply no product ions at proline rule at.
`void`	`setnPeaksInDoubleChargeWindow(Integer nPeaksInDoubleChargeWindow)` Sets the number of peaks in doubly charged windows.
`void`	`setnPeaksInSingleChargeWindow(Integer nPeaksInSingleChargeWindow)` Sets the number of peaks in singly charged windows.
`void`	`setPtmIndex(String modificationName, int ptmIndex)` Sets the index for a given modification.
`void`	`setPtmIndexes(PtmSettings modificationProfile)` Set the PTM indexes of the modifications searched.
`void`	`setRemovePrecursor(Boolean removePrecursor)` Sets whether the precursor shall be removed for OMSSA.
`void`	`setScalePrecursor(Boolean scalePrecursor)` Sets whether the precursor shall be scaled for OMSSA.
`void`	`setSearchForwardFragmentFirst(Boolean searchForwardFragmentFirst)` Sets whether forward ions (b1) should be searched first.
`void`	`setSearchPositiveIons(Boolean searchPositiveIons)` Sets whether positive ions are searched.
`void`	`setSearchRewindFragments(Boolean searchRewindFragments)` Sets whether C-terminal fragments should be searched.
`void`	`setSelectedOutput(String selectedOutput)` Sets the output type, omx, csv or pepXML.
`void`	`setSingleChargeWindow(Integer singleChargeWindow)` Sets the window size for singly charged ions.
`void`	`setUseCorrelationCorrectionScore(Boolean useCorrelationCorrectionScore)` Sets whether the correlation correction score should be used.
`String`	`toString(boolean html)` Returns the parameters as a string.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - OmssaParameters
```
public OmssaParameters()
```
    Constructor.
- Method Detail
  - getMaxEValue
```
public Double getMaxEValue()
```
    Returns the maximal e-value searched for.
    
    Returns:
    
    the maximal e-value searched for
  - setMaxEValue
```
public void setMaxEValue(Double maxEValue)
```
    Sets the maximal e-value searched for.
    
    Parameters:
    
    maxEValue - the maximal e-value searched for
  - getHitListLength
```
public Integer getHitListLength()
```
    Returns the length of the hit list for OMSSA.
    
    Returns:
    
    the length of the hit list for OMSSA
  - setHitListLength
```
public void setHitListLength(Integer hitListLength)
```
    Sets the length of the hit list for OMSSA.
    
    Parameters:
    
    hitListLength - the length of the hit list for OMSSA
  - getMinimalChargeForMultipleChargedFragments
```
public Charge getMinimalChargeForMultipleChargedFragments()
```
    Returns the minimal precursor charge to account for multiply charged fragments in OMSSA.
    
    Returns:
    
    the minimal precursor charge to account for multiply charged fragments in OMSSA
  - setMinimalChargeForMultipleChargedFragments
```
public void setMinimalChargeForMultipleChargedFragments(Charge minimalChargeForMultipleChargedFragments)
```
    Sets the minimal precursor charge to account for multiply charged fragments in OMSSA.
    
    Parameters:
    
    minimalChargeForMultipleChargedFragments - the minimal precursor charge to account for multiply charged fragments in OMSSA
  - 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
  - isEstimateCharge
```
public Boolean isEstimateCharge()
```
    Indicates whether the precursor charge shall be estimated for OMSSA.
    
    Returns:
    
    a boolean indicating whether the precursor charge shall be estimated for OMSSA
  - setEstimateCharge
```
public void setEstimateCharge(Boolean estimateCharge)
```
    Sets whether the precursor charge shall be estimated for OMSSA.
    
    Parameters:
    
    estimateCharge - a boolean indicating whether the precursor charge shall be estimated for OMSSA
  - isRemovePrecursor
```
public Boolean isRemovePrecursor()
```
    Indicates whether the precursor shall be removed for OMSSA.
    
    Returns:
    
    a boolean indicating whether the precursor shall be removed for OMSSA
  - setRemovePrecursor
```
public void setRemovePrecursor(Boolean removePrecursor)
```
    Sets whether the precursor shall be removed for OMSSA.
    
    Parameters:
    
    removePrecursor - a boolean indicating whether the precursor shall be removed for OMSSA
  - isScalePrecursor
```
public Boolean isScalePrecursor()
```
    Indicates whether the precursor shall be scaled for OMSSA.
    
    Returns:
    
    a boolean indicating whether the precursor shall be scaled for OMSSA
  - setScalePrecursor
```
public void setScalePrecursor(Boolean scalePrecursor)
```
    Sets whether the precursor shall be scaled for OMSSA.
    
    Parameters:
    
    scalePrecursor - a boolean indicating whether the precursor shall be scaled for OMSSA
  - getSelectedOutput
```
public String getSelectedOutput()
```
    Returns the selected output type, omx, csv or pepXML.
    
    Returns:
    
    the selected output type
  - setSelectedOutput
```
public void setSelectedOutput(String selectedOutput)
```
    Sets the output type, omx, csv or pepXML.
    
    Parameters:
    
    selectedOutput - the output type
  - getOmssaOutputTypes
```
public static String[] getOmssaOutputTypes()
```
    Returns the output types available.
    
    Returns:
    
    the output types available
  - isMemoryMappedSequenceLibraries
```
public Boolean isMemoryMappedSequenceLibraries()
```
    Indicates whether sequence libraries should be mapped in memory.
    
    Returns:
    
    a boolean indicating whether sequence libraries should be mapped in memory
  - setMemoryMappedSequenceLibraries
```
public void setMemoryMappedSequenceLibraries(Boolean memoryMappedSequenceLibraries)
```
    Sets whether sequence libraries should be mapped in memory.
    
    Parameters:
    
    memoryMappedSequenceLibraries - a boolean indicating whether sequence libraries should be mapped in memory
  - getNeutronThreshold
```
public Double getNeutronThreshold()
```
    Returns the mass after which exact neutron mass should be considered in the calculation.
    
    Returns:
    
    the mass after which exact neutron mass should be considered in the calculation
  - setNeutronThreshold
```
public void setNeutronThreshold(Double neutronThreshold)
```
    Sets the mass after which exact neutron mass should be considered in the calculation.
    
    Parameters:
    
    neutronThreshold - the mass after which exact neutron mass should be considered in the calculation
  - getLowIntensityCutOff
```
public Double getLowIntensityCutOff()
```
    Returns the low intensity cut-off as percentage of the most intense ion peak.
    
    Returns:
    
    the low intensity cut-off as percentage of the most intense ion peak
  - setLowIntensityCutOff
```
public void setLowIntensityCutOff(Double lowIntensityCutOff)
```
    Sets the low intensity cut-off as percentage of the most intense ion peak.
    
    Parameters:
    
    lowIntensityCutOff - the low intensity cut-off as percentage of the most intense ion peak
  - getHighIntensityCutOff
```
public Double getHighIntensityCutOff()
```
    Returns the high intensity cut-off as percentage of the most intense ion peak.
    
    Returns:
    
    the high intensity cut-off as percentage of the most intense ion peak
  - setHighIntensityCutOff
```
public void setHighIntensityCutOff(Double highIntensityCutOff)
```
    Sets the high intensity cut-off as percentage of the most intense ion peak.
    
    Parameters:
    
    highIntensityCutOff - the high intensity cut-off as percentage of the most intense ion peak
  - getIntensityCutOffIncrement
```
public Double getIntensityCutOffIncrement()
```
    Returns the intensity cut-off increment.
    
    Returns:
    
    the intensity cut-off increment
  - setIntensityCutOffIncrement
```
public void setIntensityCutOffIncrement(Double intensityCutOffIncrement)
```
    Sets the intensity cut-off increment.
    
    Parameters:
    
    intensityCutOffIncrement - the intensity cut-off increment
  - getSingleChargeWindow
```
public Integer getSingleChargeWindow()
```
    Returns the window size for singly charged ions.
    
    Returns:
    
    the window size for singly charged ions
  - setSingleChargeWindow
```
public void setSingleChargeWindow(Integer singleChargeWindow)
```
    Sets the window size for singly charged ions.
    
    Parameters:
    
    singleChargeWindow - the window size for singly charged ions
  - getDoubleChargeWindow
```
public Integer getDoubleChargeWindow()
```
    Returns the window size for doubly charged ions.
    
    Returns:
    
    the window size for doubly charged ions
  - setDoubleChargeWindow
```
public void setDoubleChargeWindow(Integer doubleChargeWindow)
```
    Sets the window size for doubly charged ions.
    
    Parameters:
    
    doubleChargeWindow - the window size for doubly charged ions
  - getnPeaksInSingleChargeWindow
```
public Integer getnPeaksInSingleChargeWindow()
```
    Returns the number of peaks in singly charged windows.
    
    Returns:
    
    the number of peaks in singly charged windows
  - setnPeaksInSingleChargeWindow
```
public void setnPeaksInSingleChargeWindow(Integer nPeaksInSingleChargeWindow)
```
    Sets the number of peaks in singly charged windows.
    
    Parameters:
    
    nPeaksInSingleChargeWindow - the number of peaks in singly charged windows
  - getnPeaksInDoubleChargeWindow
```
public Integer getnPeaksInDoubleChargeWindow()
```
    Returns the number of peaks in doubly charged windows.
    
    Returns:
    
    the number of peaks in doubly charged windows
  - setnPeaksInDoubleChargeWindow
```
public void setnPeaksInDoubleChargeWindow(Integer nPeaksInDoubleChargeWindow)
```
    Sets the number of peaks in doubly charged windows.
    
    Parameters:
    
    nPeaksInDoubleChargeWindow - the number of peaks in doubly charged windows
  - getMaxHitsPerSpectrumPerCharge
```
public Integer getMaxHitsPerSpectrumPerCharge()
```
    Returns the maximal number of hits searched per spectrum and per charge.
    
    Returns:
    
    the maximal number of hits searched per spectrum and per charge
  - setMaxHitsPerSpectrumPerCharge
```
public void setMaxHitsPerSpectrumPerCharge(Integer maxHitsPerSpectrumPerCharge)
```
    Set the maximal number of hits searched per spectrum and per charge.
    
    Parameters:
    
    maxHitsPerSpectrumPerCharge - the maximal number of hits searched per spectrum and per charge
  - getnAnnotatedMostIntensePeaks
```
public Integer getnAnnotatedMostIntensePeaks()
```
    Returns the minimal number of annotated most intense peaks.
    
    Returns:
    
    the minimal number of annotated most intense peaks
  - setnAnnotatedMostIntensePeaks
```
public void setnAnnotatedMostIntensePeaks(Integer nAnnotatedMostIntensePeaks)
```
    Sets the minimal number of annotated most intense peaks.
    
    Parameters:
    
    nAnnotatedMostIntensePeaks - the minimal number of annotated most intense peaks
  - getMinAnnotatedPeaks
```
public Integer getMinAnnotatedPeaks()
```
    Returns the minimal number of annotated peaks a peptide should have.
    
    Returns:
    
    the minimal number of annotated peaks a peptide should have
  - setMinAnnotatedPeaks
```
public void setMinAnnotatedPeaks(Integer minAnnotatedPeaks)
```
    Sets the minimal number of annotated peaks a peptide should have.
    
    Parameters:
    
    minAnnotatedPeaks - the minimal number of annotated peaks a peptide should have
  - getMinPeaks
```
public Integer getMinPeaks()
```
    Returns the minimal number of peaks a spectrum should contain.
    
    Returns:
    
    the minimal number of peaks a spectrum should contain
  - setMinPeaks
```
public void setMinPeaks(Integer minPeaks)
```
    Sets the minimal number of peaks a spectrum should contain.
    
    Parameters:
    
    minPeaks - the minimal number of peaks a spectrum should contain
  - isCleaveNterMethionine
```
public Boolean isCleaveNterMethionine()
```
    Indicates whether N-terminal methionines should be cleaved.
    
    Returns:
    
    a boolean indicating whether N-terminal methionines should be cleaved
  - setCleaveNterMethionine
```
public void setCleaveNterMethionine(Boolean cleaveNterMethionine)
```
    Sets whether N-terminal methionines should be cleaved.
    
    Parameters:
    
    cleaveNterMethionine - whether N-terminal methionines should be cleaved
  - getMaxMzLadders
```
public Integer getMaxMzLadders()
```
    Returns the maximal m/z ladder length.
    
    Returns:
    
    the maximal m/z ladder length
  - setMaxMzLadders
```
public void setMaxMzLadders(Integer maxMzLadders)
```
    Sets the maximal m/z ladder length.
    
    Parameters:
    
    maxMzLadders - the maximal m/z ladder length
  - getMaxFragmentCharge
```
public Integer getMaxFragmentCharge()
```
    Returns the maximal fragment charge.
    
    Returns:
    
    the maximal fragment charge
  - setMaxFragmentCharge
```
public void setMaxFragmentCharge(Integer maxFragmentCharge)
```
    Sets the maximal fragment charge.
    
    Parameters:
    
    maxFragmentCharge - the maximal fragment charge
  - getFractionOfPeaksForChargeEstimation
```
public Double getFractionOfPeaksForChargeEstimation()
```
    Returns the fraction of peaks to be retained for charge >1 estimation.
    
    Returns:
    
    the fraction of peaks to be retained for charge >1 estimation
  - setFractionOfPeaksForChargeEstimation
```
public void setFractionOfPeaksForChargeEstimation(Double fractionOfPeaksForChargeEstimation)
```
    Sets the fraction of peaks to be retained for charge >1 estimation.
    
    Parameters:
    
    fractionOfPeaksForChargeEstimation - the fraction of peaks to be retained for charge >1 estimation
  - isDetermineChargePlusOneAlgorithmically
```
public Boolean isDetermineChargePlusOneAlgorithmically()
```
    Indicates whether charge plus one should be determined algorithmically.
    
    Returns:
    
    whether charge plus one should be determined algorithmically
  - setDetermineChargePlusOneAlgorithmically
```
public void setDetermineChargePlusOneAlgorithmically(Boolean determineChargePlusOneAlgorithmically)
```
    Sets whether charge plus one should be determined algorithmically.
    
    Parameters:
    
    determineChargePlusOneAlgorithmically - whether charge plus one should be determined algorithmically
  - isSearchPositiveIons
```
public Boolean isSearchPositiveIons()
```
    Indicates whether positive ions are searched. False means negative ions.
    
    Returns:
    
    a boolean indicating whether positive ions are searched
  - setSearchPositiveIons
```
public void setSearchPositiveIons(Boolean searchPositiveIons)
```
    Sets whether positive ions are searched. False means negative ions.
    
    Parameters:
    
    searchPositiveIons - a boolean indicating whether positive ions are searched
  - getMinPrecPerSpectrum
```
public Integer getMinPrecPerSpectrum()
```
    Returns the minimal number of precursors per spectrum.
    
    Returns:
    
    the minimal number of precursors per spectrum
  - setMinPrecPerSpectrum
```
public void setMinPrecPerSpectrum(Integer minPrecPerSpectrum)
```
    Sets the minimal number of precursors per spectrum.
    
    Parameters:
    
    minPrecPerSpectrum - the minimal number of precursors per spectrum
  - isSearchForwardFragmentFirst
```
public Boolean isSearchForwardFragmentFirst()
```
    Indicates whether forward ions (b1) should be searched first.
    
    Returns:
    
    a boolean indicating whether forward ions (b1) should be searched first
  - setSearchForwardFragmentFirst
```
public void setSearchForwardFragmentFirst(Boolean searchForwardFragmentFirst)
```
    Sets whether forward ions (b1) should be searched first.
    
    Parameters:
    
    searchForwardFragmentFirst - whether forward ions (b1) should be searched first
  - isSearchRewindFragments
```
public Boolean isSearchRewindFragments()
```
    Indicates whether C-terminal fragments should be searched.
    
    Returns:
    
    a boolean indicating whether C-terminal fragments should be searched
  - setSearchRewindFragments
```
public void setSearchRewindFragments(Boolean searchRewindFragments)
```
    Sets whether C-terminal fragments should be searched.
    
    Parameters:
    
    searchRewindFragments - whether C-terminal fragments should be searched
  - getMaxFragmentPerSeries
```
public Integer getMaxFragmentPerSeries()
```
    Returns the maximal number of fragments to retain per series.
    
    Returns:
    
    the maximal number of fragments to retain per series
  - setMaxFragmentPerSeries
```
public void setMaxFragmentPerSeries(Integer maxFragmentPerSeries)
```
    Sets the maximal number of fragments to retain per series.
    
    Parameters:
    
    maxFragmentPerSeries - the maximal number of fragments to retain per series
  - isUseCorrelationCorrectionScore
```
public Boolean isUseCorrelationCorrectionScore()
```
    Indicates whether the correlation correction score should be used.
    
    Returns:
    
    a boolean indicating whether the correlation correction score should be used
  - setUseCorrelationCorrectionScore
```
public void setUseCorrelationCorrectionScore(Boolean useCorrelationCorrectionScore)
```
    Sets whether the correlation correction score should be used.
    
    Parameters:
    
    useCorrelationCorrectionScore - a boolean indicating whether the correlation correction score should be used
  - getConsecutiveIonProbability
```
public Double getConsecutiveIonProbability()
```
    Returns the consecutive ion probability.
    
    Returns:
    
    the consecutive ion probability
  - setConsecutiveIonProbability
```
public void setConsecutiveIonProbability(Double consecutiveIonProbability)
```
    Set the consecutive ion probability.
    
    Parameters:
    
    consecutiveIonProbability - the consecutive ion probability
  - getIterativeSequenceEvalue
```
public Double getIterativeSequenceEvalue()
```
    Returns the e-value threshold to use to consider a sequence for the iterative search. 0.0 means all.
    
    Returns:
    
    the e-value threshold to use to consider a sequence for the iterative search
  - setIterativeSequenceEvalue
```
public void setIterativeSequenceEvalue(Double iterativeSequenceEvalue)
```
    Sets the e-value threshold to use to consider a sequence for the iterative search. 0.0 means all.
    
    Parameters:
    
    iterativeSequenceEvalue - the e-value threshold to use to consider a sequence for the iterative search
  - getIterativeReplaceEvalue
```
public Double getIterativeReplaceEvalue()
```
    Returns the e-value threshold to use to replace a hit for the iterative search. 0.0 means the best hit will be retained.
    
    Returns:
    
    the e-value threshold to use to replace a hit for the iterative search
  - setIterativeReplaceEvalue
```
public void setIterativeReplaceEvalue(Double iterativeReplaceEvalue)
```
    Sets the e-value threshold to use to replace a hit for the iterative search. 0.0 means the best hit will be retained.
    
    Parameters:
    
    iterativeReplaceEvalue - the e-value threshold to use to replace a hit for the iterative search
  - getIterativeSpectrumEvalue
```
public Double getIterativeSpectrumEvalue()
```
    Returns the e-value threshold to use consider a spectrum for the iterative search. 0.0 means all.
    
    Returns:
    
    the e-value threshold to use consider a spectrum for the iterative search
  - setIterativeSpectrumEvalue
```
public void setIterativeSpectrumEvalue(Double iterativeSpectrumEvalue)
```
    Sets the e-value threshold to use consider a spectrum for the iterative search. 0.0 means all.
    
    Parameters:
    
    iterativeSpectrumEvalue - the e-value threshold to use consider a spectrum for the iterative search
  - getNoProlineRuleSeries
```
public ArrayList<Integer> getNoProlineRuleSeries()
```
    Returns the id numbers of ion series to apply no product ions at proline rule at.
    
    Returns:
    
    the id numbers of ion series to apply no product ions at proline rule at
  - setNoProlineRuleSeries
```
public void setNoProlineRuleSeries(ArrayList<Integer> noProlineRuleSeries)
```
    Sets the id numbers of ion series to apply no product ions at proline rule at.
    
    Parameters:
    
    noProlineRuleSeries - the id numbers of ion series to apply no product ions at proline rule at
  - setPtmIndex
```
public void setPtmIndex(String modificationName,
                        int ptmIndex)
```
    Sets the index for a given modification. If another modification was already given with the same index the previous setting will be silently overwritten.
    
    Parameters:
    
    modificationName - the name of the modification
    
    ptmIndex - the index of the modification
  - getModificationName
```
public String getModificationName(int ptmIndex)
```
    Returns the name of the modification indexed by the given index. Null if not found.
    
    Parameters:
    
    ptmIndex - the index of the modification to look for
    
    Returns:
    
    the name of the modification indexed by the given index
  - hasPtmIndexes
```
public boolean hasPtmIndexes()
```
    Indicates whether the modification profile has PTM indexes.
    
    Returns:
    
    true if an PTM indexes map is set
  - getPtmIndex
```
public Integer getPtmIndex(String modificationName)
```
    Returns the index of a given modification, null if not found.
    
    Parameters:
    
    modificationName - the name of the modification
    
    Returns:
    
    the corresponding index
  - getPtmIndexes
```
public HashMap<Integer,String> getPtmIndexes()
```
    Returns the PTM indexes as a map.
    
    Returns:
    
    the PTM indexes
  - setPtmIndexes
```
public void setPtmIndexes(PtmSettings modificationProfile)
```
    Set the PTM indexes of the modifications searched.
    
    Parameters:
    
    modificationProfile - the modification profile of this search
  - getOMSSAIndexes
```
public static HashMap<String,Integer> getOMSSAIndexes(File modificationsFile)
                                               throws org.xmlpull.v1.XmlPullParserException,
                                                      FileNotFoundException,
                                                      IOException
```
    Imports the OMSSA indexes from an XML file.
    
    Parameters:
    
    modificationsFile - the modification file
    
    Returns:
    
    a map of all indexes: modification name > OMSSA index
    
    Throws:
    
    org.xmlpull.v1.XmlPullParserException - if an XmlPullParserException occurs
    
    FileNotFoundException - if a FileNotFoundException occurs
    
    IOException - if an IOException occurs
  - 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

Class OmssaParameters

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

OmssaParameters

Method Detail

getMaxEValue

setMaxEValue

getHitListLength

setHitListLength

getMinimalChargeForMultipleChargedFragments

setMinimalChargeForMultipleChargedFragments

getMaxPeptideLength

setMaxPeptideLength

getMinPeptideLength

setMinPeptideLength

isEstimateCharge

setEstimateCharge

isRemovePrecursor

setRemovePrecursor

isScalePrecursor

setScalePrecursor

getSelectedOutput

setSelectedOutput

getOmssaOutputTypes

isMemoryMappedSequenceLibraries

setMemoryMappedSequenceLibraries

getNeutronThreshold

setNeutronThreshold

getLowIntensityCutOff

setLowIntensityCutOff

getHighIntensityCutOff

setHighIntensityCutOff

getIntensityCutOffIncrement

setIntensityCutOffIncrement

getSingleChargeWindow

setSingleChargeWindow

getDoubleChargeWindow

setDoubleChargeWindow

getnPeaksInSingleChargeWindow

setnPeaksInSingleChargeWindow

getnPeaksInDoubleChargeWindow

setnPeaksInDoubleChargeWindow

getMaxHitsPerSpectrumPerCharge

setMaxHitsPerSpectrumPerCharge

getnAnnotatedMostIntensePeaks

setnAnnotatedMostIntensePeaks

getMinAnnotatedPeaks

setMinAnnotatedPeaks

getMinPeaks

setMinPeaks

isCleaveNterMethionine

setCleaveNterMethionine

getMaxMzLadders

setMaxMzLadders

getMaxFragmentCharge

setMaxFragmentCharge

getFractionOfPeaksForChargeEstimation

setFractionOfPeaksForChargeEstimation

isDetermineChargePlusOneAlgorithmically

setDetermineChargePlusOneAlgorithmically

isSearchPositiveIons

setSearchPositiveIons

getMinPrecPerSpectrum

setMinPrecPerSpectrum

isSearchForwardFragmentFirst

setSearchForwardFragmentFirst

isSearchRewindFragments

setSearchRewindFragments

getMaxFragmentPerSeries

setMaxFragmentPerSeries

isUseCorrelationCorrectionScore

setUseCorrelationCorrectionScore

getConsecutiveIonProbability

setConsecutiveIonProbability

getIterativeSequenceEvalue

setIterativeSequenceEvalue

getIterativeReplaceEvalue

setIterativeReplaceEvalue