public enum PsmScores extends Enum<PsmScores>
Enum Constant and Description |
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aa_intensity
The intensity sub-score as adapted from the DirecTag paper
(http://www.ncbi.nlm.nih.gov/pubmed/18630943) per amino acid.
|
aa_ms2_mz_fidelity
The m/z fidelity score as adapted from the DirecTag paper
(http://www.ncbi.nlm.nih.gov/pubmed/18630943) per amino acid.
|
complementarity
The complementarity score as adapted from the DirecTag paper
(http://www.ncbi.nlm.nih.gov/pubmed/18630943).
|
intensity
The intensity sub-score as adapted from the DirecTag paper
(http://www.ncbi.nlm.nih.gov/pubmed/18630943).
|
ms2_mz_fidelity
The m/z fidelity score as adapted from the DirecTag paper
(http://www.ncbi.nlm.nih.gov/pubmed/18630943).
|
native_score
The native score of the search engine.
|
precursor_accuracy
The precursor accuracy.
|
Modifier and Type | Field and Description |
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boolean |
increasing
Indicates whether the score increases with the quality of the match.
|
int |
index
The index of the score of interest.
|
String |
name
The name of the score.
|
Modifier and Type | Method and Description |
---|---|
static double |
getDecreasingScore(Peptide peptide,
Integer peptideCharge,
MSnSpectrum spectrum,
ShotgunProtocol shotgunProtocol,
IdentificationParameters identificationParameters,
SpecificAnnotationSettings specificAnnotationPreferences,
int scoreIndex)
Scores the match between the given peptide and spectrum using the given
score.
|
static PsmScores |
getScore(int scoreIndex)
Returns the PSM score of the given index.
|
static double |
getScore(Peptide peptide,
Integer peptideCharge,
MSnSpectrum spectrum,
ShotgunProtocol shotgunProtocol,
IdentificationParameters identificationParameters,
SpecificAnnotationSettings specificAnnotationPreferences,
int scoreIndex)
Scores the match between the given peptide and spectrum using the given
score.
|
static double |
getScore(Peptide peptide,
Integer peptideCharge,
MSnSpectrum spectrum,
ShotgunProtocol shotgunProtocol,
IdentificationParameters identificationParameters,
SpecificAnnotationSettings specificAnnotationPreferences,
PsmScores psmScore)
Scores the match between the given peptide and spectrum using the given
score.
|
static PsmScores |
valueOf(String name)
Returns the enum constant of this type with the specified name.
|
static PsmScores[] |
values()
Returns an array containing the constants of this enum type, in
the order they are declared.
|
public static final PsmScores native_score
public static final PsmScores precursor_accuracy
public static final PsmScores ms2_mz_fidelity
public static final PsmScores aa_ms2_mz_fidelity
public static final PsmScores intensity
public static final PsmScores aa_intensity
public static final PsmScores complementarity
public final String name
public final int index
public final boolean increasing
public static PsmScores[] values()
for (PsmScores c : PsmScores.values()) System.out.println(c);
public static PsmScores valueOf(String name)
name
- the name of the enum constant to be returned.IllegalArgumentException
- if this enum type has no constant with the specified nameNullPointerException
- if the argument is nullpublic static PsmScores getScore(int scoreIndex)
scoreIndex
- the index of the desired scorepublic static double getDecreasingScore(Peptide peptide, Integer peptideCharge, MSnSpectrum spectrum, ShotgunProtocol shotgunProtocol, IdentificationParameters identificationParameters, SpecificAnnotationSettings specificAnnotationPreferences, int scoreIndex)
peptide
- the peptide of interestpeptideCharge
- the charge of the peptidespectrum
- the spectrum of interestshotgunProtocol
- information on the protocol usedidentificationParameters
- the identification parametersspecificAnnotationPreferences
- the annotation preferences specific
to this psmscoreIndex
- the index of the score to usepublic static double getScore(Peptide peptide, Integer peptideCharge, MSnSpectrum spectrum, ShotgunProtocol shotgunProtocol, IdentificationParameters identificationParameters, SpecificAnnotationSettings specificAnnotationPreferences, int scoreIndex)
peptide
- the peptide of interestpeptideCharge
- the charge of the peptidespectrum
- the spectrum of interestshotgunProtocol
- information on the protocol usedidentificationParameters
- the identification parametersspecificAnnotationPreferences
- the annotation preferences specific
to this psmscoreIndex
- the index of the score to usepublic static double getScore(Peptide peptide, Integer peptideCharge, MSnSpectrum spectrum, ShotgunProtocol shotgunProtocol, IdentificationParameters identificationParameters, SpecificAnnotationSettings specificAnnotationPreferences, PsmScores psmScore)
peptide
- the peptide of interestpeptideCharge
- the charge of the peptidespectrum
- the spectrum of interestshotgunProtocol
- information on the protocol usedidentificationParameters
- the identification parametersspecificAnnotationPreferences
- the annotation preferences specific
to this psmpsmScore
- the score to useCopyright © 2016. All rights reserved.