Class PeptideAssumptionFilter
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
- All Implemented Interfaces:
Serializable
public class PeptideAssumptionFilter extends ExperimentObject
This class filters peptide assumptions based on various properties.
- Author:
- Marc Vaudel, Harald Barsnes
- See Also:
- Serialized Form
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Field Summary
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Constructor Summary
Constructors Constructor Description PeptideAssumptionFilter()
Constructor with default settings.PeptideAssumptionFilter(int minPepLength, int maxPepLength, double maxMzDeviation, boolean isPpm, boolean unknownModification, Integer minMissedCleavages, Integer maxMissedCleavages, Integer minIsotopes, Integer maxIsotopes)
Constructor for an Identification filter. -
Method Summary
Modifier and Type Method Description Integer
getMaxIsotopes()
Returns the maximal number of isotopes allowed (inclusive).Integer
getMaxMissedCleavages()
Returns the maximum number of missed cleavages.double
getMaxMzDeviation()
Returns the maximal m/z deviation allowed.int
getMaxPepLength()
Returns the maximal peptide length allowed.Integer
getMinIsotopes()
Returns the minimal number of isotopes allowed (inclusive).Integer
getMinMissedCleavages()
Returns the minimum number of missed cleavages.int
getMinPepLength()
Returns the maximal peptide length allowed.String
getShortDescription()
Returns a short description of the parameters.boolean
isIsPpm()
Indicates whether the mass tolerance is in ppm (true) or Dalton (false).boolean
isSameAs(PeptideAssumptionFilter anotherFilter)
Indicates whether this filter is the same as another one.boolean
removeUnknownModifications()
Returns a boolean indicating whether unknown modifications shall be removed.void
setFilterFromSearchParameters(SearchParameters searchParameters)
Updates the filter based on the search parameters.void
setIsPpm(boolean isPpm)
Sets whether the mass tolerance is in ppm (true) or Dalton (false).void
setMaxIsotopes(Integer maxIsotopes)
Sets the maximal number of isotopes allowed (inclusive).void
setMaxMissedCleavages(Integer maxMissedCleavages)
Set the maximum number of missed cleavages.void
setMaxMzDeviation(double maxMzDeviation)
Sets the maximal m/z deviation allowed.void
setMaxPepLength(int maxPepLength)
Sets the maximal peptide length allowed.void
setMinIsotopes(Integer minIsotopes)
Sets the minimal number of isotopes allowed (inclusive).void
setMinMissedCleavages(Integer minMissedCleavages)
Set the minimum number of missed cleavages.void
setMinPepLength(int minPepLength)
Sets the maximal peptide length allowed.void
setRemoveUnknownModifications(boolean unknownModification)
Set whether unknown modifications shall be removed.boolean
validateModifications(Peptide peptide, SequenceMatchingParameters sequenceMatchingPreferences, SequenceMatchingParameters modificationSequenceMatchingPreferences, ModificationParameters modificationProfile)
Verifies that the definition of every modification name is available.boolean
validatePeptide(Peptide peptide, SequenceMatchingParameters sequenceMatchingPreferences, DigestionParameters digestionPreferences)
Validates the peptide based on the peptide length, the share of X's in the sequence and the allowed number of missed cleavages.boolean
validatePrecursor(PeptideAssumption assumption, String spectrumFile, String spectrumTitle, SpectrumProvider spectrumProvider, SearchParameters searchParameters)
Validates the mass deviation of a peptide assumption.boolean
validateProteins(Peptide peptide, SequenceMatchingParameters sequenceMatchingPreferences, SequenceProvider sequenceProvider)
Validates a peptide depending on its protein inference status.Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
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Constructor Details
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PeptideAssumptionFilter
public PeptideAssumptionFilter()Constructor with default settings. -
PeptideAssumptionFilter
public PeptideAssumptionFilter(int minPepLength, int maxPepLength, double maxMzDeviation, boolean isPpm, boolean unknownModification, Integer minMissedCleavages, Integer maxMissedCleavages, Integer minIsotopes, Integer maxIsotopes)Constructor for an Identification filter.- Parameters:
minPepLength
- the minimal peptide length allowed (0 or less for disabled)maxPepLength
- the maximal peptide length allowed (0 or less for disabled)maxMzDeviation
- the maximal m/z deviation allowed (0 or less for disabled)isPpm
- boolean indicating the unit of the allowed m/z deviation (true: ppm, false: Da)unknownModification
- shall peptides presenting unknown modifications be removedminMissedCleavages
- the minimum number of missed cleavages allowed (null for disabled)maxMissedCleavages
- the maximum number of missed cleavages allowed (null for disabled)minIsotopes
- the minimum number of isotopes allowed (null for disabled)maxIsotopes
- the maximum number of isotopes allowed (null for disabled)
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Method Details
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setFilterFromSearchParameters
Updates the filter based on the search parameters.- Parameters:
searchParameters
- the search parameters where to take the information from
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validatePeptide
public boolean validatePeptide(Peptide peptide, SequenceMatchingParameters sequenceMatchingPreferences, DigestionParameters digestionPreferences)Validates the peptide based on the peptide length, the share of X's in the sequence and the allowed number of missed cleavages.- Parameters:
peptide
- the peptide to validatesequenceMatchingPreferences
- the sequence matching preferences containing the maximal share of X's alloweddigestionPreferences
- the digestion preferences- Returns:
- a boolean indicating whether the peptide passed the test
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validateProteins
public boolean validateProteins(Peptide peptide, SequenceMatchingParameters sequenceMatchingPreferences, SequenceProvider sequenceProvider)Validates a peptide depending on its protein inference status.- Parameters:
peptide
- the peptidesequenceMatchingPreferences
- the sequence matching preferencessequenceProvider
- a sequence provider- Returns:
- a boolean indicating whether the peptide passed the test
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validateModifications
public boolean validateModifications(Peptide peptide, SequenceMatchingParameters sequenceMatchingPreferences, SequenceMatchingParameters modificationSequenceMatchingPreferences, ModificationParameters modificationProfile)Verifies that the definition of every modification name is available.- Parameters:
peptide
- the peptide of interestsequenceMatchingPreferences
- the sequence matching preferences for peptide to protein mappingmodificationSequenceMatchingPreferences
- the sequence matching preferences for modification to peptide mappingmodificationProfile
- the modification profile of the identification- Returns:
- a boolean indicating whether the peptide passed the test
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validatePrecursor
public boolean validatePrecursor(PeptideAssumption assumption, String spectrumFile, String spectrumTitle, SpectrumProvider spectrumProvider, SearchParameters searchParameters)Validates the mass deviation of a peptide assumption.- Parameters:
assumption
- the considered peptide assumptionspectrumFile
- the file of the spectrum used to get the precursorspectrumTitle
- the file of the spectrum used to get the precursorspectrumProvider
- the spectrum providersearchParameters
- the search parameters- Returns:
- a boolean indicating whether the given assumption passes the filter
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removeUnknownModifications
public boolean removeUnknownModifications()Returns a boolean indicating whether unknown modifications shall be removed.- Returns:
- a boolean indicating whether unknown modifications shall be removed
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setRemoveUnknownModifications
public void setRemoveUnknownModifications(boolean unknownModification)Set whether unknown modifications shall be removed.- Parameters:
unknownModification
- whether unknown modifications shall be removed
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isIsPpm
public boolean isIsPpm()Indicates whether the mass tolerance is in ppm (true) or Dalton (false).- Returns:
- a boolean indicating whether the mass tolerance is in ppm (true) or Dalton (false)
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setIsPpm
public void setIsPpm(boolean isPpm)Sets whether the mass tolerance is in ppm (true) or Dalton (false).- Parameters:
isPpm
- a boolean indicating whether the mass tolerance is in ppm (true) or Dalton (false)
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getMaxMzDeviation
public double getMaxMzDeviation()Returns the maximal m/z deviation allowed.- Returns:
- the maximal mass deviation allowed
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setMaxMzDeviation
public void setMaxMzDeviation(double maxMzDeviation)Sets the maximal m/z deviation allowed.- Parameters:
maxMzDeviation
- the maximal mass deviation allowed
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getMaxPepLength
public int getMaxPepLength()Returns the maximal peptide length allowed.- Returns:
- the maximal peptide length allowed
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setMaxPepLength
public void setMaxPepLength(int maxPepLength)Sets the maximal peptide length allowed.- Parameters:
maxPepLength
- the maximal peptide length allowed
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getMinPepLength
public int getMinPepLength()Returns the maximal peptide length allowed.- Returns:
- the maximal peptide length allowed
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setMinPepLength
public void setMinPepLength(int minPepLength)Sets the maximal peptide length allowed.- Parameters:
minPepLength
- the maximal peptide length allowed
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getMinIsotopes
Returns the minimal number of isotopes allowed (inclusive).- Returns:
- the minimal number of isotopes allowed
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setMinIsotopes
Sets the minimal number of isotopes allowed (inclusive).- Parameters:
minIsotopes
- the minimal number of isotopes allowed
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getMaxIsotopes
Returns the maximal number of isotopes allowed (inclusive).- Returns:
- the maximal number of isotopes allowed
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setMaxIsotopes
Sets the maximal number of isotopes allowed (inclusive).- Parameters:
maxIsotopes
- the maximal number of isotopes allowed
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isSameAs
Indicates whether this filter is the same as another one.- Parameters:
anotherFilter
- another filter- Returns:
- a boolean indicating that the filters have the same parameters
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getShortDescription
Returns a short description of the parameters.- Returns:
- a short description of the parameters
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getMinMissedCleavages
Returns the minimum number of missed cleavages. Null means no limit.- Returns:
- the minMissedCleavages
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setMinMissedCleavages
Set the minimum number of missed cleavages. Null means no limit.- Parameters:
minMissedCleavages
- the minMissedCleavages to set
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getMaxMissedCleavages
Returns the maximum number of missed cleavages. Null means no limit.- Returns:
- the maxMissedCleavages
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setMaxMissedCleavages
Set the maximum number of missed cleavages. Null means no limit.- Parameters:
maxMissedCleavages
- the maxMissedCleavages to set
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