public class PeptideAssumptionFilter extends ExperimentObject
NO_KEY
Constructor and 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.
|
Modifier and Type | Method and 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.
|
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
public PeptideAssumptionFilter()
public PeptideAssumptionFilter(int minPepLength, int maxPepLength, double maxMzDeviation, boolean isPpm, boolean unknownModification, Integer minMissedCleavages, Integer maxMissedCleavages, Integer minIsotopes, Integer maxIsotopes)
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)public void setFilterFromSearchParameters(SearchParameters searchParameters)
searchParameters
- the search parameters where to take the
information frompublic boolean validatePeptide(Peptide peptide, SequenceMatchingParameters sequenceMatchingPreferences, DigestionParameters digestionPreferences)
peptide
- the peptide to validatesequenceMatchingPreferences
- the sequence matching preferences
containing the maximal share of X's alloweddigestionPreferences
- the digestion preferencespublic boolean validateProteins(Peptide peptide, SequenceMatchingParameters sequenceMatchingPreferences, SequenceProvider sequenceProvider)
peptide
- the peptidesequenceMatchingPreferences
- the sequence matching preferencessequenceProvider
- a sequence providerpublic boolean validateModifications(Peptide peptide, SequenceMatchingParameters sequenceMatchingPreferences, SequenceMatchingParameters modificationSequenceMatchingPreferences, ModificationParameters modificationProfile)
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 identificationpublic boolean validatePrecursor(PeptideAssumption assumption, String spectrumFile, String spectrumTitle, SpectrumProvider spectrumProvider, SearchParameters searchParameters)
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 parameterspublic boolean removeUnknownModifications()
public void setRemoveUnknownModifications(boolean unknownModification)
unknownModification
- whether unknown modifications shall be removedpublic boolean isIsPpm()
public void setIsPpm(boolean isPpm)
isPpm
- a boolean indicating whether the mass tolerance is in ppm
(true) or Dalton (false)public double getMaxMzDeviation()
public void setMaxMzDeviation(double maxMzDeviation)
maxMzDeviation
- the maximal mass deviation allowedpublic int getMaxPepLength()
public void setMaxPepLength(int maxPepLength)
maxPepLength
- the maximal peptide length allowedpublic int getMinPepLength()
public void setMinPepLength(int minPepLength)
minPepLength
- the maximal peptide length allowedpublic Integer getMinIsotopes()
public void setMinIsotopes(Integer minIsotopes)
minIsotopes
- the minimal number of isotopes allowedpublic Integer getMaxIsotopes()
public void setMaxIsotopes(Integer maxIsotopes)
maxIsotopes
- the maximal number of isotopes allowedpublic boolean isSameAs(PeptideAssumptionFilter anotherFilter)
anotherFilter
- another filterpublic String getShortDescription()
public Integer getMinMissedCleavages()
public void setMinMissedCleavages(Integer minMissedCleavages)
minMissedCleavages
- the minMissedCleavages to setpublic Integer getMaxMissedCleavages()
public void setMaxMissedCleavages(Integer maxMissedCleavages)
maxMissedCleavages
- the maxMissedCleavages to setCopyright © 2021. All rights reserved.