|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectcom.compomics.util.preferences.IdFilter
public class IdFilter
This class achieves a pre-filtering of the identifications for PeptideShaker.
Constructor Summary | |
---|---|
IdFilter()
Constructor with default settings. |
|
IdFilter(int minPepLength,
int maxPepLength,
double mascotMaxEvalue,
double omssaMaxEvalue,
double xtandemMaxEvalue,
double maxMzDeviation,
boolean isPpm,
boolean unknownPTM)
Constructor for an Identification filter. |
Method Summary | |
---|---|
boolean |
equals(IdFilter anotherFilter)
Indicates whether this filter is the same as another one. |
double |
getMascotMaxEvalue()
Returns the maximal Mascot e-value allowed. |
double |
getMaxMzDeviation()
Returns the maximal m/z deviation allowed. |
int |
getMaxPepLength()
Returns the maximal peptide length allowed. |
int |
getMinPepLength()
Returns the maximal peptide length allowed. |
double |
getOmssaMaxEvalue()
Returns the OMSSA maximal e-value allowed. |
double |
getXtandemMaxEvalue()
Returns the maximal X!Tandem e-value allowed. |
boolean |
isIsPpm()
Indicates whether the mass tolerance is in ppm (true) or Dalton (false). |
boolean |
removeUnknownPTMs()
Returns a boolean indicating whether unknown PTMs shall be removed. |
void |
setIsPpm(boolean isPpm)
Sets whether the mass tolerance is in ppm (true) or Dalton (false). |
void |
setMascotMaxEvalue(double mascotMaxEvalue)
Sets the maximal Mascot e-value allowed. |
void |
setMaxMzDeviation(double maxMzDeviation)
Sets the maximal m/z deviation allowed. |
void |
setMaxPepLength(int maxPepLength)
Sets the maximal peptide length allowed. |
void |
setMinPepLength(int minPepLength)
Sets the maximal peptide length allowed. |
void |
setOmssaMaxEvalue(double omssaMaxEvalue)
Sets the OMSSA maximal e-value allowed. |
void |
setRemoveUnknownPTMs(boolean unknownPtm)
Set whether unknown PTMs shall be removed. |
void |
setXtandemMaxEvalue(double xtandemMaxEvalue)
Sets the OMSSA maximal e-value allowed. |
boolean |
validateModifications(Peptide peptide,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Validates the modifications of a peptide. |
boolean |
validatePeptideAssumption(PeptideAssumption assumption)
Validates the peptide assumption based on the peptide length and maximal e-values allowed. |
boolean |
validatePrecursor(PeptideAssumption assumption,
String spectrumKey,
SpectrumFactory spectrumFactory)
Validates the mass deviation of a peptide assumption. |
boolean |
validateProteins(Peptide peptide)
Validates a peptide depending on its protein inference status. |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
---|
public IdFilter()
public IdFilter(int minPepLength, int maxPepLength, double mascotMaxEvalue, double omssaMaxEvalue, double xtandemMaxEvalue, double maxMzDeviation, boolean isPpm, boolean unknownPTM)
minPepLength
- The minimal peptide length allowed (0 or less for
disabled)maxPepLength
- The maximal peptide length allowed (0 or less for
disabled)mascotMaxEvalue
- The maximal Mascot e-value allowed (0 or less for
disabled)omssaMaxEvalue
- The maximal OMSSA e-value allowed (0 or less for
disabled)xtandemMaxEvalue
- The maximal X!Tandem e-value 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)unknownPTM
- Shall peptides presenting unknownPTMs be ignoredMethod Detail |
---|
public boolean validatePeptideAssumption(PeptideAssumption assumption)
assumption
- the assumption to validate
public boolean validateProteins(Peptide peptide)
peptide
- the peptide
public boolean validateModifications(Peptide peptide, ProteinMatch.MatchingType matchingType, Double massTolerance)
peptide
- the peptide of interestmatchingType
- the peptide-protein matching typemassTolerance
- the mass tolerance for matching type
'indistiguishibleAminoAcids'. Can be null otherwise
public boolean validatePrecursor(PeptideAssumption assumption, String spectrumKey, SpectrumFactory spectrumFactory) throws IOException, uk.ac.ebi.jmzml.xml.io.MzMLUnmarshallerException
assumption
- the considered peptide assumptionspectrumKey
- the key of the spectrum used to get the precursor the
precursor should be accessible via the spectrum factoryspectrumFactory
- the spectrum factory
IOException
uk.ac.ebi.jmzml.xml.io.MzMLUnmarshallerException
public boolean removeUnknownPTMs()
public void setRemoveUnknownPTMs(boolean unknownPtm)
unknownPtm
- whether unknown PTMs 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 getMascotMaxEvalue()
public void setMascotMaxEvalue(double mascotMaxEvalue)
mascotMaxEvalue
- the maximal Mascot e-value allowedpublic 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 double getOmssaMaxEvalue()
public void setOmssaMaxEvalue(double omssaMaxEvalue)
omssaMaxEvalue
- the OMSSA maximal e-value allowedpublic double getXtandemMaxEvalue()
public void setXtandemMaxEvalue(double xtandemMaxEvalue)
xtandemMaxEvalue
- the OMSSA maximal e-value allowedpublic boolean equals(IdFilter anotherFilter)
anotherFilter
- another filter
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |