Class OmssaParameters
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.tool_specific.OmssaParameters
- All Implemented Interfaces:
IdentificationAlgorithmParameter
,Serializable
public class OmssaParameters extends ExperimentObject implements IdentificationAlgorithmParameter
The OMSSA specific parameters.
- Author:
- Marc Vaudel
- See Also:
- Serialized Form
-
Field Summary
-
Constructor Summary
Constructors Constructor Description OmssaParameters()
Constructor. -
Method Summary
Modifier and Type Method 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.int
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.int
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.int
getMaxFragmentCharge()
Returns the maximal fragment charge.int
getMaxFragmentPerSeries()
Returns the maximal number of fragments to retain per series.int
getMaxHitsPerSpectrumPerCharge()
Returns the maximal number of hits searched per spectrum and per charge.int
getMaxMzLadders()
Returns the maximal m/z ladder length.int
getMaxPeptideLength()
Returns the maximal peptide length allowed.int
getMinAnnotatedPeaks()
Returns the minimal number of annotated peaks a peptide should have.int
getMinimalChargeForMultipleChargedFragments()
Returns the minimal precursor charge to account for multiply charged fragments in OMSSA.int
getMinPeaks()
Returns the minimal number of peaks a spectrum should contain.int
getMinPeptideLength()
Sets the minimal peptide length allowed.int
getMinPrecPerSpectrum()
Returns the minimal number of precursors per spectrum.String
getModificationName(int ptmIndex)
Returns the name of the modification indexed by the given index.int
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.int
getnPeaksInDoubleChargeWindow()
Returns the number of peaks in doubly charged windows.int
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.int
getPtmIndex(String modificationName)
Returns the index of a given modificationHashMap<Integer,String>
getPtmIndexes()
Returns the PTM indexes as a map.String
getSelectedOutput()
Returns the selected output type, omx, csv or pepXML.int
getSingleChargeWindow()
Returns the window size for singly charged ions.boolean
hasModificationIndexes()
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(int 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(int 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(int maxFragmentCharge)
Sets the maximal fragment charge.void
setMaxFragmentPerSeries(int maxFragmentPerSeries)
Sets the maximal number of fragments to retain per series.void
setMaxHitsPerSpectrumPerCharge(int maxHitsPerSpectrumPerCharge)
Set the maximal number of hits searched per spectrum and per charge.void
setMaxMzLadders(int maxMzLadders)
Sets the maximal m/z ladder length.void
setMaxPeptideLength(int maxPeptideLength)
Sets the maximal peptide length allowed.void
setMemoryMappedSequenceLibraries(boolean memoryMappedSequenceLibraries)
Sets whether sequence libraries should be mapped in memory.void
setMinAnnotatedPeaks(int minAnnotatedPeaks)
Sets the minimal number of annotated peaks a peptide should have.void
setMinimalChargeForMultipleChargedFragments(int minimalChargeForMultipleChargedFragments)
Sets the minimal precursor charge to account for multiply charged fragments in OMSSA.void
setMinPeaks(int minPeaks)
Sets the minimal number of peaks a spectrum should contain.void
setMinPeptideLength(int minPeptideLength)
Sets the minimal peptide length allowed.void
setMinPrecPerSpectrum(int minPrecPerSpectrum)
Sets the minimal number of precursors per spectrum.void
setnAnnotatedMostIntensePeaks(int 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(int nPeaksIndoubleChargeWindow)
Sets the number of peaks in doubly charged windows.void
setnPeaksInSingleChargeWindow(int 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(ModificationParameters 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(int 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 com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
-
Constructor Details
-
OmssaParameters
public OmssaParameters()Constructor.
-
-
Method Details
-
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 int getHitListLength()Returns the length of the hit list for OMSSA.- Returns:
- the length of the hit list for OMSSA
-
setHitListLength
public void setHitListLength(int hitListLength)Sets the length of the hit list for OMSSA.- Parameters:
hitListLength
- the length of the hit list for OMSSA
-
getMinimalChargeForMultipleChargedFragments
public int 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(int 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 int getMaxPeptideLength()Returns the maximal peptide length allowed.- Returns:
- the maximal peptide length allowed
-
setMaxPeptideLength
public void setMaxPeptideLength(int maxPeptideLength)Sets the maximal peptide length allowed.- Parameters:
maxPeptideLength
- the maximal peptide length allowed
-
getMinPeptideLength
public int getMinPeptideLength()Sets the minimal peptide length allowed.- Returns:
- the minimal peptide length allowed
-
setMinPeptideLength
public void setMinPeptideLength(int 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
Returns the selected output type, omx, csv or pepXML.- Returns:
- the selected output type
-
setSelectedOutput
Sets the output type, omx, csv or pepXML.- Parameters:
selectedOutput
- the output type
-
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 int getSingleChargeWindow()Returns the window size for singly charged ions.- Returns:
- the window size for singly charged ions
-
setSingleChargeWindow
public void setSingleChargeWindow(int singleChargeWindow)Sets the window size for singly charged ions.- Parameters:
singleChargeWindow
- the window size for singly charged ions
-
getDoubleChargeWindow
public int getDoubleChargeWindow()Returns the window size for doubly charged ions.- Returns:
- the window size for doubly charged ions
-
setDoubleChargeWindow
public void setDoubleChargeWindow(int doubleChargeWindow)Sets the window size for doubly charged ions.- Parameters:
doubleChargeWindow
- the window size for doubly charged ions
-
getnPeaksInSingleChargeWindow
public int getnPeaksInSingleChargeWindow()Returns the number of peaks in singly charged windows.- Returns:
- the number of peaks in singly charged windows
-
setnPeaksInSingleChargeWindow
public void setnPeaksInSingleChargeWindow(int nPeaksInSingleChargeWindow)Sets the number of peaks in singly charged windows.- Parameters:
nPeaksInSingleChargeWindow
- the number of peaks in singly charged windows
-
getnPeaksInDoubleChargeWindow
public int getnPeaksInDoubleChargeWindow()Returns the number of peaks in doubly charged windows.- Returns:
- the number of peaks in doubly charged windows
-
setnPeaksInDoubleChargeWindow
public void setnPeaksInDoubleChargeWindow(int nPeaksIndoubleChargeWindow)Sets the number of peaks in doubly charged windows.- Parameters:
nPeaksIndoubleChargeWindow
- the number of peaks in doubly charged windows
-
getMaxHitsPerSpectrumPerCharge
public int 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(int 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 int getnAnnotatedMostIntensePeaks()Returns the minimal number of annotated most intense peaks.- Returns:
- the minimal number of annotated most intense peaks
-
setnAnnotatedMostIntensePeaks
public void setnAnnotatedMostIntensePeaks(int nAnnotatedMostIntensePeaks)Sets the minimal number of annotated most intense peaks.- Parameters:
nAnnotatedMostIntensePeaks
- the minimal number of annotated most intense peaks
-
getMinAnnotatedPeaks
public int 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(int 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 int 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(int 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 int getMaxMzLadders()Returns the maximal m/z ladder length.- Returns:
- the maximal m/z ladder length
-
setMaxMzLadders
public void setMaxMzLadders(int maxMzLadders)Sets the maximal m/z ladder length.- Parameters:
maxMzLadders
- the maximal m/z ladder length
-
getMaxFragmentCharge
public int getMaxFragmentCharge()Returns the maximal fragment charge.- Returns:
- the maximal fragment charge
-
setMaxFragmentCharge
public void setMaxFragmentCharge(int 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 int getMinPrecPerSpectrum()Returns the minimal number of precursors per spectrum.- Returns:
- the minimal number of precursors per spectrum
-
setMinPrecPerSpectrum
public void setMinPrecPerSpectrum(int 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 int 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(int 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
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
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
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 modificationptmIndex
- the index of the modification
-
getModificationName
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
-
hasModificationIndexes
public boolean hasModificationIndexes()Indicates whether the modification profile has PTM indexes.- Returns:
- true if an PTM indexes map is set
-
getPtmIndex
Returns the index of a given modification- Parameters:
modificationName
- the name of the modification- Returns:
- the corresponding index
-
getPtmIndexes
Returns the PTM indexes as a map.- Returns:
- the PTM indexes
-
setPtmIndexes
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, IOExceptionImports 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 occursFileNotFoundException
- if a FileNotFoundException occursIOException
- if an IOException occurs
-
getAlgorithm
Description copied from interface:IdentificationAlgorithmParameter
Returns the identification algorithm.- Specified by:
getAlgorithm
in interfaceIdentificationAlgorithmParameter
- Returns:
- the identification algorithm
-
equals
Description copied from interface:IdentificationAlgorithmParameter
Indicates whether another identificationAlgorithmParameter has the same parameters.- Specified by:
equals
in interfaceIdentificationAlgorithmParameter
- Parameters:
identificationAlgorithmParameter
- the other identificationAlgorithmParameter- Returns:
- true if the algorithm and parameters are the same
-
toString
Description copied from interface:IdentificationAlgorithmParameter
Returns the parameters as a string.- Specified by:
toString
in interfaceIdentificationAlgorithmParameter
- Parameters:
html
- use HTML formatting- Returns:
- the parameters as a string
-